Two Always-on-Top Apps Fighting? How to Fix Z-Order Wars

Two always-on-top apps on the same screen produce z-order wars. Each app believes it should be on top, and the OS resolves the conflict by giving the most recently activated app the topmost slot — which means whichever app you touched last wins, and the other disappears underneath. The visible symptom is one app flickering behind the other as you move the cursor between them. The invisible symptom is that one app is silently failing to receive input because the other is on top of it. This guide covers why always-on-top apps fight, how to pick one winner per screen region, and what to do with common combinations like PowerToys Always On Top and a clipboard shelf.

For neighbouring topics, see reduce motion settings and spring UIs and integrated GPUs and transparent windows.

What always-on-top actually is

WS_EX_TOPMOST is the Win32 flag that puts a window above all non-topmost windows. The flag is a z-order property: a topmost window is shown above every non-topmost window, regardless of which has focus. Among multiple topmost windows, the most recently activated one is on top.

When two apps both set WS_EX_TOPMOST, they compete for the topmost-of-topmost slot. The OS resolves this by activation order: the last app to be activated (clicked, hotkey-triggered, or programmatically foregrounded) is on top. Whichever app you used most recently wins; the other is hidden behind it.

This is the correct OS behaviour for general-purpose topmost windows. It is the wrong behaviour for two apps that both need to be visible at the same time, because they cannot both be on top.

The three common always-on-top apps

Three classes of always-on-top apps are common on Windows in 2026:

• PowerToys Always On Top — pins an arbitrary window on top via a hotkey (default Win+Ctrl+T). Useful for keeping a reference window visible while working in another. Pins one window at a time.
• Pin to Top utilities — third-party tools that do the same thing as PowerToys Always On Top, sometimes with more options (multiple pinned windows, per-window z-order).
• Clipboard shelves and overlay tools — apps that are always-on-top by design, including Edge-Drop, overshow shelves, and various sidebar tools.

The first two are opt-in per-window: the user pins a specific window. The third is opt-in by app: the app is always-on-top, period. The conflict is between two always-on-top apps, or between an always-on-top app and a pinned window.

Where the conflict actually lives

The conflict is most visible when:

• A clipboard shelf is on the right edge, and a pinned window is also on the right edge. The pinned window covers the shelf, or the shelf covers the pinned window, depending on which was activated last.
• A clipboard shelf is on the right edge, and a PowerToys Always On Top-pinned window is in the centre of the screen but extends to the right edge. The pinned window's right edge overlaps the shelf's trigger strip.
• Two clipboard shelves are running. This is rare but possible if the user is testing tools; the two shelves fight for the same edge.
• A screen-recording tool (OBS, ShareX) is set to always-on-top, and the shelf is on the same screen. The recording tool's preview window covers the shelf.

In each case, the conflict is z-order, not pixels. The two apps do not need to overlap; they need only to both be topmost. The OS resolves the conflict by activation order, which is why the symptom is "whichever I used last is on top."

Resolution patterns

Pick one winner per screen region

The simplest resolution is to assign each screen region to one always-on-top app. The right edge is the shelf's region; the centre is the user's working area; the top-left is the recording tool's preview. No region has two always-on-top apps, and the conflict does not arise.

The cost is that the user cannot pin an arbitrary window on top of the shelf's region. If the user wants to pin a reference window in the right half of the screen, they must accept that the shelf will be hidden, or move the reference window to a different region.

Suppress the shelf when a pinned window is on the same screen

A more sophisticated pattern is for the shelf to detect pinned windows on its screen and suppress itself when one is present. This requires the shelf to enumerate top-level windows periodically and check for the WS_EX_TOPMOST flag on windows that overlap its region. The cost is complexity and a small CPU overhead.

The benefit is that the user does not need to think about the conflict; the shelf gets out of the way when a pinned window is present, and returns when the pinned window is unpinned.

Disable PowerToys Always On Top

If the conflict is specifically with PowerToys Always On Top, the simplest resolution is to disable the PowerToys module. PowerToys Always On Top is a convenience, not a necessity; the user can achieve the same effect by using the app's own always-on-top setting if it has one, or by arranging windows to avoid the conflict.

Run the shelf on a different monitor

On a multi-monitor setup, the shelf can be on a monitor that does not have pinned windows. This is the cleanest separation: the shelf is always visible on its monitor, and pinned windows live on the other monitor. For the multi-monitor discussion, see clipboard tools on multi-monitor Windows setups and how to pick which monitor Edge-Drop uses.

What can go wrong

• Two always-on-top apps on the same screen, both visible. Symptom: flickering as the OS resolves the z-order conflict. Fix: pick one winner per region or move one app to a different monitor.
• A pinned window covers the shelf. Symptom: the shelf is invisible because the pinned window is on top. Fix: unpin the window, or move the shelf to a different region.
• A pinned window is hidden behind the shelf. Symptom: the pinned window is not visible because the shelf is on top. Fix: this is rare because the shelf is typically narrow; if it happens, move the shelf or unpin the window.
• PowerToys Always On Top pins the shelf itself. Symptom: the shelf is pinned and cannot be hidden. Fix: disable PowerToys Always On Top, or unpin the shelf with Win+Ctrl+T when the shelf has focus.

Multi-monitor interaction

On a multi-monitor setup, the conflict is per-monitor. A pinned window on Monitor A does not affect a shelf on Monitor B. The shelf can be on its own monitor without conflict, and the user can pin windows freely on the other monitors.

The exception is when a pinned window is large enough to span monitors. A maximised pinned window covers all monitors it spans, and the shelf on any of those monitors is hidden. The fix is to use windowed pinned windows, or to put the shelf on a monitor that the pinned window does not span.

For the related discussion of fullscreen exclusive mode (which is a separate suppression), see gaming fullscreen and clipboard hotkeys and should a clipboard app hide in games.

Honest positioning

Edge-Drop, the Windows hover-activated clipboard shelf, is always-on-top by design — it cannot be hidden behind other windows, because its purpose is to be reachable from any working state. The shelf uses WS_EX_TOPMOST for the open state and WS_EX_TRANSPARENT | WS_EX_LAYERED for the collapsed state, so when collapsed it does not cover other windows even though it is on top in z-order. The shelf does not currently detect or respond to other always-on-top apps on the same screen; the user is expected to manage the z-order by not pinning windows that overlap the shelf's region. For users who need pinned windows on the same screen as the shelf, the recommendation is to disable PowerToys Always On Top or to use a multi-monitor setup where the shelf and the pinned windows live on different monitors.

What to check

If your always-on-top apps are fighting, work through these:

1. List the always-on-top apps on the screen. (Common: clipboard shelf, PowerToys Always On Top, screen recording tool, sticky notes.)
2. Identify which regions each app occupies.
3. Where two apps share a region, decide which is the winner. Move or disable the loser.
4. Test by activating each app in turn; the winner should remain visible.
5. If the conflict is between the shelf and a pinned window, unpin the window or move the shelf.

The right answer is one always-on-top app per screen region. More than one produces the z-order war, and the only way to win is not to play.

Related reading

• Integrated GPUs and Transparent Windows
• Clipboard Tools on Multi-Monitor Windows Setups
• Win+V Not Working on Windows 11: 9 Fixes
• How to Enable Clipboard History in Windows 11

Sources

• Microsoft Learn — Window z-order — Win32 reference for the WS_EX_TOPMOST flag and how z-order is resolved among topmost windows
• Microsoft Learn — SetWindowPos — Win32 reference for the function used to change a window's z-order, including the HWND_TOPMOST constant
• Microsoft Learn — Layered windows — Win32 reference for the WS_EX_LAYERED and WS_EX_TRANSPARENT combination used by collapsed overlays
• Microsoft Learn — PowerToys — official documentation for PowerToys, including the Always On Top module
• Microsoft Learn — EnumWindows — Win32 reference for the API an app uses to enumerate top-level windows and check their z-order flags

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