What I will do is try and format the SD card with the phone, then put everything back on. So far, I have isolated it to ESFile explorer. Initially I did not update the apk and thought that would work. It did not.
Here's what has happened:
I use ESFile explorer to access the SD card. Then when I went into clockworkmod, I tried to delete a nandroid copy I made. It says 'failed to delete'.
Then the ROM and sdCard do not work correctly anymore, so I have to wipe and re-flash an old nandroid.
Makes me wonder if something is corrupted in the SD Card. Everything used to work fine, but now whenever I access the SD Card with ESFile explorer, even the old version of it, it causes issue.