I had 6 water barrels under rain for about 10 minutes and none of them filled, not even partially.

It's working on my end in the plains biome. Make sure it's not in the desert.

Report issues again if you're still having this problem.

Still having it.

Try spawning in a barrel and see if that one fills.

Spawned in ones still don't fill with water, alas.

Are you able to put fluids inside?

Yes, (Tried water bucket)

Ok, so water is visible in the barrel when placing it in manually? Can you create a new world and try it with rain?

Yep and you can take the water out of the barrel. I'll create a local world and see what happens.

Ok a local world, using the same files I uploaded to the server, works fine. So is there something else beside the config/mod (minus the nonserver mods)/world folders I'm supposed to update when updating on the server side?

mods I removed from the server mod folder are:
Custom main menu
Hardcore map reset
Launch GUI
Resource loader
Mousetweaks

I honestly have no idea... I'll look into this in the morning.