I don't have SDL manually installed, and the only thing i can think of is that i am using ATI Remote Wonder with it's official Windows drivers (and their app). I tried it on two computers with Windows XP SP3 and it happens on both.
Let me know what else i can do to help figure out what's going on.
I also tried without having the remote plugged in (and also closed ATI's app for the remote), but the problem persists. When the mouse is disabled (even though there is still an X-like cursor, but clicking doesn't work in this case), the only problem is a flickering square (around 64x64) in the bottom right corner of the screen, and it flickers between what should be displayed and what is below the app (a black wallpaper on my desktop in my case). When the mouse is enabled on the other hand, the cursor constantly flickers and a box (like described before) also flickers and keeps following the mouse (so around the mouse is around 64x64 box which keeps flickering). Even when the mouse is disabled, the box still follows it, but it's only visible on any moving parts or animations. It looks kind of like, if you take an animation, record the part that is animating, and switch every 2nd or 3rd frame with a black image (or whatever the wallpaper or program beneath XBMC looks like).
Also, on the scrolling text at the bottom for example, the black box is only flickering (coming trough) on the far right part of the screen, but if i move the mouse to another part over the text, it only keeps flickering the "old" state trough (like take what was there 2 sec ago and show that instead of what should be there now, but there is no black color coming trough here). Also i noticed that until i move the mouse, the same content keeps flickering over (so if i moved the mouse over the text "Trackers moved from", as long as i don't move the mose, it keeps flickering this text, even though the text is moving, or even when the text runs out and there's only gray background).
I could not move the mouse, but still i have this black box on the far bottom left corner which keeps flickering with my background (i.e. wallpaper), even when i don't move the mouse, or the cursor is somewhere else. When the cursor is there, it flickers faster, but when it's somewhere else it still flickers, just slower.
This is a video of the problem:
http://zeta.mrbrdo.net/test.avi (~2MB)
The framerate is very low, so please note it actually flickers very fast, and on the video it may seem as if the "wrong thing" is just displayed all the time, but in fact it actually flickers very fast, in all cases. Also at the very end you can see even the yellow square animation is also flickering, even though it is barely noticable on the video. This whole video is taken with mouse disabled in XBMC (so you see the X-Windows cursor). With the mouse enabled it's just worse, the cursor also flickers all the time and there is more flickering going on. The video starts just after i run XBMC, so you can see how the desktop shortcut is coming trough. But later if i move my mouse there it isn't coming trough anymore, since there is no animation or moving parts at that part of the screen. I am using the release version of XBMC for Windows, i downloaded it around 2 days ago.