Didn't have these issues using 2.5.1:9998 or anything lower than that.

Edit: After digging much deeper I have more info, I didn't know my hardware.

Windows XP SP 3
Nvidia 9800 GT
4GB Ram
AMD Athlon Dual Core 2.7GHZ

and I can't get the command prompt thing to work. Keeps annoying me about -basedir or some crap. Everlasting windows problems...

Edit: Forgot. yes I do know about r_fog r_water r_showtris and all the rest of the stuff. I tried the r_water and the same thing keeps happening. Also tried redownloading...

Tried it on suse too. works fine there I'll just use that. But thats still an issue maybe for some people.

http://forums.alientrap.local/viewtopic.php?t=5477 have a look . this is fixed in svn . also the hot fix is comming soon .

a quick fix for me has been to set r_water 0 to 1

yeah I tried that but I still got the error spam and "spermy water"

No worries though. Just thought I better let you know. I'll switch back to 9998 for the time being

Have a look at this circle around the problem with white waters.

http://alientrap.org/forum/viewtopic.php?p=70423&highlight=#70423