[ponicg]

The problem here is EXT4. You're on Midnight ROM 4 which uses EXT4. EXT4 is a journaling filesystem, so changes are buffered. Hard shutdowns such as when phone falls and battery pops out, when the phone locks and you have to shut it off, or one other case I'll outline below can cause the journal to go bad and the filesystem to become partially corrupt. I don't think Android does an fsck when it boots, but you might be able finnegale it into doing so.

I've purchased the 2x batteries + wall charger from EBAY, so I switch batteries all the time. I hardly ever use the microUSB port. Here's a word of advice:

When switching batteries, do a regular software power down(hold the power button ,hit power-down then ok) and WAIT FOR THE PHONE TO VIBRATE. Only when you feel the vibrate is the phone actually off, and it's ok to swap batteries.