Okay, this is pretty weird (I didn't have this problem in my first playthrough)... I just played through the bandit fortress outer wall battle, and rain wasn't animating for me during the actual fight. It worked OK during the deployment phase and the intro, but as soon as I got control, it stopped.
Here's a GIF of it in action... or rather inaction.
http://gfycat.com/EmbellishedAdventurousAlpinegoat
I force-generated a log file, though I don't think it's logged anywhere. I'm running 1.0.39, steam version.
Thanks! I'll look into this ASAP. :)
This is now fixed going forward into the next update.