Mods getting turned off after a patch is by design. Every time a patch comes out, it tends to break mods. Playing with broken mods can cause some major problems, including breaking saves, which I'm SURE none of us want. This is a GOOD thing. You should always leave it off after an update until you verify all your installed mods are updated and working properly.
However, if you turn mods back on and it keeps getting turned back off, THAT is a known bug. It never happened to me, but I'm told it's due to a corruption in the options.ini file. If you delete the Options.ini file, the game will recreate it and it should work again.
