Well I've had weird things happen when flashing stuff (I was using the "new-cwm.zip") , seemed like data being written where it shouldn't be? Just flashing theme files or own stuff I want to add, and I've had the following stuff happen:
Nuked my radio, had an unknown baseband and calls would never work, fortunately Radio Odin fixed it.
Had some /data apps disappear. Had some /data/data disappear. On reboot had Setup Wizard pop-up, even though I still had my Google account registered.
Hoping this new clockwork is completely safe. I suspected that clockwork was responsible for my weird happenings, so data-wiped and haven't flashed anything, so far fine functioning.