Well, depending on how much time you have on your hands, and everything is backed up. You could use mattlgrof's utility to flash your firmware back to stock, reroot, dont accept OTA, then freeze the OTAupdater with an app like Titanuim backup so you don't get/have to worry about accidently accepting the OTA. And you wouldn't be bothered with the notifications if you use the stock ROM This works even better if CM11 is your daily driver, and you don't really use stock. I assume you are on BMM? If you are on safestrap, you can flash the stock slot with CM11.
If you still have the problem, you will at least know it wasn't the OTA.