Window mode sometimes turns into a slideshow.

As in 1fps. Works just fine other times. With no changing of any options or anything besides resizing and stuff. Only when I turn on AA. Full Screen works perfect. Just Window mode is sporatic.

A64 3200+
1GB Generic RAM
X800XL

There is your problem right there, you have generic RAM! (lol)

No seriously, AA combined with programs running in the background (if any), can cause a drop in FPS as you are describing.

What resolution are you running it at? If it is at something like 1600x1200 with AA/AF then you need to tune it down a notch.

I run A64 3400+ w/ 1gb Corsiar Ram and FX 5700 Ultra and run 1024x768 w/ 4x AA turned on. The quality bar is around 75% max.

Also check your refresh rate and make sure it matches your mointer setting.

I have a different problem
Every time I play windowed, it works for 3-5 minutes and reboots my computer

My system:
Athlon 64 2800+
OCZ Ultra High Performance RAM 1 Gb
XFX GeForce 6600 GT 128 Mb

Full cooling installed from Zalman and Arctic Cooling so I have no idea why that happens...

It's working fine now. But it'll screw up later. How annoying...

Do you have any programs like Konfabulator, WindowBlinds, WindowFX, or anything that uses alpha-transparency running on your desktop? If you do that can interfere with antialiasing in windowed mode. I have the same problem.