Trouble installing stock ROM due to multiple '0' folders !HELP!
From what you describe, the most likely cause is that your flash storage no longer applies any writes – be it additions or deletions. For understanding, a simply description of what happens:


You send a file to the storage (copy/flash).
to be most responsive, the OS uses "buffers" in RAM to cache your storage, so that's where the file goes first.
You check if the file arrived, and the OS says it did (but in fact, it just saw it in the "buffer pending to be written")
Now the OS tries to "flush" the buffers (write them to "disk"), but fails
As long as the buffer "lives", you won't notice. But as soon as you write more than the buffer can hold, the oldest entries disappear. On boot, the entire buffer disappears.


So in the end, that was the reason why CM "suddenly stopped working": the storage got unusable. And this is also the reason why your device booted up into CM after you thought you've flashed another ROM: the flash was never performed.

I had this twice with SD cards, a replacement was in order then. Unfortunately, internal storage is soldered in into your device, so you cannot simply replace it: you'd have to send-in the device to have its board replaced. Unless the device is still in warranty (which I very much doubt if we speak about the 2011 "Galaxy Nexus", code-named "Maguro" here), it's probably not worth the postage costs, but you'll rather have to get yourself a replacement device – which might even be cheaper than the repair.