Sometimes I have the same prob - but when I restart my computer, delete all temporary files with C-Cleaner and started the PupilCommander new - it works again.
The best is, when you make an Export every day, so long the PupilCommander runs - if one day the DB is maybe corrupted, you can delete all, import the file from "yesterday" and it works again sure. So you have only one day difference.
Good luck