The PhatHack DMS Tools doesn't have a verification option?

I would run a disk check on the PHTDTA partition as it sounds like something might be going wrong there, and this might tell you if there is something more serious going on. You might want to copy anything you need to keep off the cartridge first though.
Once you've backed up everything you need, try reformatting PHTDTA. IF you are not confident with this you'll have to wait for a little while until I have the GM firmware available in the tools which I'm hoping won't be long, and then you can try the DMS Tools to do a DMS Repair.
Sam, if you are watching, does the hack do GM boxes?