When we encountered this issue, our first thought was to clear the PaperPort metadata, and look for a possibly corrupted PDF. Turns out the source issue here had nothing to do with these usual troubleshooting items.

We viewed PaperPort's activity in Process Explorer and it was file collisions with a number of TMP files in the user's temp directory (%temp%).

Purging the temporary files got PaperPort working again. If this becomes a common recurrance, we recommend a batch file or script to clear out at least the PaperPort temp files. On our subject system, the files were ZNPxxxx.tmp. Even a shortcut should suffice with the command: del "%temp%\ZNP*.TMP"