I'm also getting this problem, Just FYI, I'm using steam and am using the proper mod file. the C\ users etc path, several mods (such as the pickle+spice mod set, Zspawn and crafting helper) and a few others, they all list on the mods selection page on the main menu, yet some (namely the ones I just listed) are unticked when I reboot. Checking the Loaded.txt I see that the names are listed as C:\User(blah blah)\[CraftingHelper] (for example) wheras the mods that remain ticked are simply listed as CraftingHelper (Once again just an example) I'm doing a full re-installation as I type this, I mean uninstalling the game from steam AND deleting the actual files from C:\User\(Etc) I'll post to see how it goes after installing just ONE of the mods that kept unselecting, and see how it goes.