1. When switching windows in WinEQ sometimes the mouse doesn't re-capture right away. So you have the Windows XP cursor floating above the windows for about a second before you can move the game cursor.
2. Sometimes when switching windows a Tooltip box will be visible on the screen. As in a little beige box saying "Maximize", "Close", "Minimize", etc. This may have something to do with the first bug.
3. If you minimize a WinEQ window and then switch to another WinEQ window sometimes you cannot use the Cycle Next Window key to switch back. You have to release the mouse and then click the window button on the task bar.
4. This one is a little hard to explain but here it goes... If you release the mouse on a window sometimes you cannot click left anything, no taskbar buttons, the start button, nothing. The only way I've been able to fix this is to right click the WinEQ systray icon and open up the default settings (selecting anything with a right click might work) and then just cliking "Ok" again.
5. Keys tend to get stuck if you're holding them down while switching windows. Like if you switch windows while holding down ALT sometimes you have to tap it again or the game thinks the button is still pressed. I'm not sure if this is a bug in WinEQ or maybe EQ itself.
6. When I enter a heavy load area (PoK, the Bazaar) and I start getting bit framey I'll see the WinEQ context menu popup. Sometimes the key I was pressing before the framiness (not sure if that's a word...) began will become stuck. ex. If I'm pressing the up arrow to move forward and then go into a framey area I can let off the up arrow and I'll still be running forward.
That's all I can think of at the moment. Hope it helps and hope everything I listed wasn't mentioned before.

Machine specs: Intel 3.0 Gig, Asus P4C800 Deluxe, GeForce 5900 Ultra, 1 Gig Dual Channel DDR, Windows XP Pro