Thanks!
Pretty much. I had roughly 20 mods installed, and I noticed my EVE clouds weren't working and I had some time to kill, so I opened up a fresh install of KSP with EVE and nothing else. I added mods one at a time until it stopped working, and the two problem mods ended up being Tarsier and RCSBuildAid. Installing either one of those kills the clouds and uninstalling fixes them. I was confused too, which is why I asked.