Well, I did some testing by exporting my entire modlist into a .ckan file, then proceeded to delete my gamedata folder, validating my KSP install, then use CKAN to reinstall my entire modlist from the .ckan file.
Still, same issue.
I figured it was worth a shot.
After looking around some more, I suddenly noticed something strange. Somehow I had two different versions of Universal storage at the same time... DOH!
It turns out that Universal Storage and Universal storage 2 together, is a really bad idea.
After removing one of them, everything is back to normal.
I could have sworn I never installed Universal storage myself, but I guess I must have done so by accident when updating my mods. Fat fingers FTW!