Looks like I'm going to have to use the drive builder on my drives to get it all back to normal.

Except for removing all third-party software, which is presumably not what you had in mind, the disk builder won't do anything to solve this problem.

You can test whether your disk is dying with

dd if=/dev/hda3 of=/dev/null bs=512

If it completes without error and says

33264+0 records in
33264+0 records out

then your disk is (at least for current purposes) fine.

Peter