ISSUE 

Forum Threads:
http://forums.steampowered.com/forums/showthread.php?t=1346269

Some users report flickering window border in Jedi Knight. This seems to affect some users who use ddraw_(hack_viewport3_clear2).zip.

SOLUTION

Close or minimize every other program or window you have open. Also, anything that causes a popup, like a messenger program or other alert will cause the window border to start to flicker when you get a message or alert.

"Setting jk.exe and jedi.exe to "disable visual themes" and "disable desktop composition" in the compatibility tab for each helped - still some flickering, and a little square in top right, but not as bad as without."
http://forums.steampowered.com/forums/showthread.php?t=975224&page=2