Generating pages is a very resource intensive activity so it sounds like your system is experiencing resource issues when processing so many pdf files.  If increasing your system resources is not a possibility, try scanning in your largest pdf files in smaller batches.

As for the error “Could not find a part of the path”, there could be a few reason why you are receiving this message such as how the temp documents are being saved or interference from a third party application. I would suggest you bring both of these issues up with your VAR since they have a better understanding of your environment and can perform live troubleshooting.