Hope this hasn't been posted already...just trying to help those who have this issue like i did. For me rain effects weren't showing up in the game at all (intro level, seat of power level, etc.) until i put this command into my autoexec.cfg file:

r_UseMergedPosts=0

After that voila! Rain in all the proper levels. Be warned though that this work around makes r_UseEdgeAA=3 completely useless as it messes up the graphics....edgeAA 1 or 2 work fine though. This work around also seems to make sunshafts more pronounced.....some might like that some may not.

Also for those who might want a havier rain effect try raising r_RainAmount=1 to a higher number. I like the rain at about 1.5 but higher adds more so change it to your liking.

Okay, hope this helps others out like it did for me.

Thanks for this, I noticed I was missing rain and this fixed the problem for me. Do we lose anything by turning it off?