There's a really annoying bug in multiple versions of Windows where sometimes the system tray tooltips and popup notifications will show up behind the taskbar, or behind other windows:

It's documented in Microsoft's Knowledge Base, but I find the proposed solutions a bit lacking:
To resolve this issue, use one of the following methods:
- Log off and then log back on to the current account.
- Restart your computer.
I'm constantly getting bitten by this bug, so I developed a little program to fix it. What it does is apply the style HWND_TOPMOST to all windows that have the class name tooltips_class32, solving the problem (temporarily):
SetTopmost PROC hWnd :HWND
; we just need to apply HWND_TOPMOST, the window procedure for the tooltip
; automatically sets the size, position, and visibility of the control
INVOKE SetWindowPos, hWnd, HWND_TOPMOST, 0, 0, 0, 0, SWP_NOMOVE OR SWP_NOSIZE OR SWP_NOACTIVATE
ret
SetTopmost ENDP
Maybe I could modify it so that it runs in the background, sending a message every few minutes...
Well, for now this is what you have: tooltips.zip (source included, as always).
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