Basically just like the title says the nights are wayy longer than the day, and it rains every night, but only at night.
I'm not sure if it's Quark but it's one of the mods I have on the server and I didn't know where to ask for help otherwise.
The mods are:

Refined storage
Pixelmon
Project Red
Dimensional doors
Travelers backpacks
Reliquary
JEI
Bibliocraft
Decocraft
ComputerCraft
Draconic Evolution
Extra Utilities 2
Iron Chest
Quark
Tinkers construct

There is nothing in the console that indicated what mod it could be, nor could I find anything in the config files. Please help.

This is definitely nor quark.

I'd try removing mods one by one starting with ones that might affect weather to see which is the culprit.