r_aa_blit
 

When I remove the "#" from in front of "r_aa_blit 1" in the included eq2.ini file, the game loads fine, but if I go to windowed mode my ui disappears until I go back to full screen mode. Any ideas?

Possible suggestions are...

1) Don't use AA (leave that line commented) if you intend to go windowed
2) If you're using an nVidia card, try using the current beta drivers instead of the current WHQL driver.
3) If 2) is not the case, go back to 1.

This assumes that your UI disappearing is due to the UI flickering issue with current nVidia WHQL drivers. If that's not the case, #1 is the only thing I can suggest.