I had the same problem with my box tonight. I've had my Xbox modded and working great for about five months now, and tonight it just crapped out. I was playing Tiger Woods 2003 (from the hard drive), and in the middle I received the "the disc you are using is dirty or damaged" message. Upon rebooting, the default MS dash came up rather than XBMP (which I've been using lately as my primary dash). I used my EvoX boot disk and ftp'd to find that my F drive was empty. I restored EvoX to the C partition, rebooted, disabled the F drive, rebooted, re-enabled the F drive, and now everything seems to be working again, thankfully.
I have a Maxtor 120 Gb drive, locked, with about 60 Gb free on F. Curiously, EvoX reported the correct free disk space on F although it couldn't access anything. My ftp program showed the full free disk space on F (as if it was completely wiped out). I'm not sure what caused it to freak out, but it has me a little worried.