There's some control for this in the eq2ui_windowelements.xml file somewhere. I tried dropping in the old file at one point and my tooltip boxes actually went black - probably more due to not finding something than legitimately changing the colour
- but I did actually find that preferable to the awful red. With all the other things I've had to faff with to try and get my UI back to normal I didn't have the patience to follow this up.
If you dig around in there and find a fix please post back to let the rest of us know