Default [Q] Fixing broken file system

Yesterday some apps started to act up (e.g. the terminal emulator that wouldn't start or root-apps that claimed that they could not write to secured locations even though I granted them root), so I rebooted the phone. After that it came back on looking like after a factory reset. There was that Droid I had to press and it wanted me to sign on with my Google account. All my apps were gone (except of the originally installed ones).
Terminal emulator still wouldn't start, WLAN wouldn't connect and after a reboot it would have forgotten every change I did.
Under Manage Apps it would report that the internal storage was filled 0% of 0 MB.
When I received a text it would tell me that my Text Message Storage was full, even though there wasn't a single text in the inbox (they got deleted aswell).

I figure the file system is broken. Do you have any idea what I could do to recover that partition / the data on it?

I am running an XT860, Minimoto 1.7, Safestrap 3 (don't know what version exactly)

Stock ROM is fine.