Check the following things:

1. Make sure you aren't trying to record directly to a slow external drive (e.g. Zip), are you? That can easily do it.
2. Do you have the variable speed function activated?
3. Is something accidentally plugged into the foot pedal socket?
4. Do two external devices have the same SCSI address?
5. Is some external SCSI device hogging the processing time?
6. Is a MIDI device taking control of the timing?

The most likely cause seems to be that the hard drive is struggling with a slightly damaged format.
1. Upgrade to v1.10.
2. Back up your work - assuming 788 can do it with a damaged format (copying to the other partition should help). Make 2 copies if you can.
3. Format the hard drive, as has been suggested here after an upgrade.
4. Restore your work to the hard drive.

If this does not work, then it seems that one of these might be the cause:
1. The hard drive is damaged.
2. The hard drive is so fragmented that it can't keep up - formatting as in 2-4 above cures this.
3. Moisture condensing inside 788 is affecting the clock circuits.

- The "impossible" has happened and your song has somehow overloaded the DSP capabilities of 788. It is always a slim possibility when dealing with digital real-time processing.