I've found that the problem was still occuring during the nightly backup. I had setup a different group to test run with so I didn't run a backup on most of the servers which are in the same backup. The ExchangeIS backup is fine now after deleting all Networker software and reinstalling manually with the addon for ExchIS. The normal file system backup would sometimes only backup one drive out of 3 or none, and it was random. I could run a backup straight after the one before it and get different results. I had also found that there were errors on the exchange server relating to VSS, so I reset all the VSS on each drive but that didn't make any difference to the backup.

I've found that after setting the machine as a virtual machine with the settings and specifying logon credentials, that it still wasn't working properly. I just had my first night backup that worked fine, a normal incremental. I changed the backup group to retry upto 3 times, and it seems after 1 retry it works fine, though this hasn't solved the cause of the issue, it is just a work around now.

If anyone has any further information on the cause, I'd be happy to hear it.