When always on top stops working on Windows 11, it is almost always one of five things: another window is also topmost, the window you are covering runs as administrator, a game is in exclusive fullscreen, a Remote Desktop or VM window is topmost itself, or the pin was lost because the app restarted. PinPoint helps with the last two kinds of problem most: it shows a colored border so you can see what is pinned, and its auto-pinning rules re-pin an app every time it launches. For the rest, the fix is a setting, not a different tool.
Below is each cause, how to recognize it, and what actually fixes it.
Pin any window with a hotkey, see it with a colored border, and re-pin it automatically on launch.
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What does “always on top” actually do in Windows?
Every always on top tool, from PowerToys to PinPoint, uses the same Windows feature: the topmost flag. Microsoft’s SetWindowPos documentation defines it: HWND_TOPMOST “places the window above all non-topmost windows,” and “the window maintains its topmost position even when it is deactivated.”
The key words are “non-topmost.” Topmost is a band, not a single top spot. A pinned window stays above ordinary windows, but if two windows are both topmost, Windows orders them among themselves. That one rule explains most of the failures below.
Why does my pinned window go behind another window?
Because the other window is topmost too. Microsoft says this directly in the PowerToys Always On Top documentation: “Always On Top can’t guarantee that the window will be above other topmost windows.”
Common topmost windows you may not think of:
| Window | Why it is topmost |
|---|---|
| Video call mini windows | Apps keep a small call view above other windows |
| Screen recording and capture toolbars | So the controls stay reachable |
| Some media players’ compact mode | Built-in “on top” option |
| Remote Desktop, Citrix, VMware | Listed by Microsoft as possibly topmost (see below) |
| Another pinning tool | Two tools pinning the same window, or different ones |
Fix: decide which one should win. Turn off the other app’s own “on top” option, or unpin and re-pin the window you want in front. Running two pinning tools at once also causes confusion; pick one.
Why can’t I pin a window that runs as administrator?
Windows does not let a normal app move or resize windows that belong to an elevated (administrator) app. Microsoft’s PowerToys administrator mode page lists “Always On Top: Pin windows that are elevated” as a case that needs admin mode, and says PowerToys may not function with elevated apps in focus “unless it’s elevated as well.”
How to recognize it: the hotkey works on most windows but does nothing on Task Manager, an elevated terminal, Registry Editor, or an installer.
Fix options:
- Run the target app without elevation if it does not actually need admin rights.
- Run the pinning tool as administrator for that session, accepting the security trade-off. Microsoft notes that running apps as administrator “may expose your system to security risks.”
- Live with it for occasional admin windows. Most reference windows (browser, PDF, notes, video) are not elevated.
This applies to any pinning tool that runs as a normal user, PinPoint included.
Why does my pinned window disappear when I start a game?
There are two different things going on.
Exclusive fullscreen. Microsoft’s DirectX team explains in Demystifying Fullscreen Optimizations that Fullscreen Exclusive mode “gives your game complete ownership of the display,” and that overlays in that mode may cause “performance regressions, instability and issues with anti-cheat.” A pinned desktop window is not drawn over a true exclusive fullscreen game.
Borderless windowed. In borderless or windowed mode the Desktop Window Manager stays in control, so normal topmost windows can sit above the game. Microsoft’s Fullscreen Optimizations run many fullscreen games this way behind the scenes.
Fix: switch the game to borderless windowed in its graphics settings if you want a timer, chat, or guide visible on top. On a second monitor, a pinned window on the other screen is unaffected either way.
Also check your tool’s game setting. PowerToys Always On Top has a “Do not activate when Game Mode is on” option, which, as the docs say, “prevents the feature from being activated when actively playing a game.”
Why does a pinned window go behind Remote Desktop or a VM?
Microsoft lists three known cases in the PowerToys Always On Top compatibility table: Citrix (issue 15680), RDP (issue 16631), and VMware (issue 18834), each with the note that these windows “may be topmost, so a pinned window might appear behind them.”
Fix: if you run a remote session full screen, put your pinned window on another monitor, or use the remote session in a window. Inside the remote session, pins apply to that remote desktop, not to your local one.
Set a rule once and PinPoint pins the app every time it opens, with no hotkey to remember.
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Why did my window stop being on top after I reopened it?
The topmost flag belongs to a window, not to an app. Close the app, or let it restart after an update, and the new window starts as a normal window. Manual pinning tools (a hotkey or a menu click) need you to pin it again every time.
This is the problem PinPoint’s Intelligent Auto-Pinning is built for. You select an app from the running process list, and PinPoint pins it automatically when it launches. Workspace Pin Profiles save a set of pinned apps for a context, so you can switch between, for example, a “Research” and a “Development” setup in one click.
Fix: use per-app auto-pin rules for the windows you always want on top, and keep the hotkey for one-off pins.
Quick diagnosis table
| Symptom | Likely cause | Fix |
|---|---|---|
| Pin works, but one specific window stays in front | Both are topmost | Turn off the other window’s on top option |
| Hotkey does nothing on Task Manager or an elevated terminal | Elevated target | Run the tool as admin, or run the target unelevated |
| Pinned window vanishes in a game | Exclusive fullscreen | Use borderless windowed, or a second monitor |
| Pinned window hidden by RDP, Citrix, or VMware | Remote window is topmost | Window the session, or pin on another screen |
| Pin is gone after app restart | New window, no flag | Auto-pin rule per app |
| Not sure what is pinned | No visual cue | Use a tool with a border indicator |
How does PinPoint compare with PowerToys Always On Top here?
PowerToys Always On Top is free, well documented, and does the core job with Win+Ctrl+T, a colored border, and an excluded apps list. If you pin a window now and then, it is a fine choice.
PinPoint is a paid, one-time purchase app focused on automation. From its Store listing:
- Intelligent Auto-Pinning pins chosen apps automatically when they launch.
- Workspace Pin Profiles switch whole sets of pins at once.
- Application Exclusion Rules are there so, in the listing’s words, secondary utility panels or system alerts never accidentally interrupt your focus.
- Timed Countdown Release unpins a window automatically after a set time.
- Custom borders and audio feedback show and confirm what is pinned.
- Less than 14 MB on disk, offline, no telemetry, no account.
Neither tool can beat the Windows rules above: both are limited by elevated windows, exclusive fullscreen, and other topmost windows. Our full PinPoint vs PowerToys Always On Top comparison covers the rest.
Frequently asked questions
Can any app force a window above an exclusive fullscreen game?
Not as a normal desktop window. Exclusive fullscreen gives the game ownership of the display. Use borderless windowed mode or a second monitor.
Why does always on top work in one app and not another?
Usually because the second app runs as administrator, or because it is already topmost and wins the order.
Does PinPoint remember pins after a reboot?
Auto-pin rules apply whenever the target app launches while PinPoint is running, so rule-based pins come back after a reboot or app restart without a hotkey.
Does PinPoint send any data?
No. It runs offline with no telemetry and no account.
Try PinPoint
Get PinPoint from the Microsoft Store as a one-time purchase, or read more on the PinPoint product page. New to pinning? Start with how to keep a window always on top in Windows 11.
Keep the windows you need in front, automatically, every time they open.
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Microsoft, Windows, PowerToys, and DirectX are trademarks of the Microsoft group of companies. Citrix and VMware are trademarks of their respective owners. Other product names are trademarks of their owners. PinPoint is not affiliated with or endorsed by any of them.
Last updated 17 October 2026. Published by Automata Labs, a software company in Canada.