Notes/Domino 6 and 7 Forum : Unknown Agent Error following Upgrade

We recently upgraded our Domino server to 6.5 from 5.0.12. Only a handful of clients have been upgraded. My databases have all been upgraded (now have ODS = 43 instead of 41, which I've been told means they are 6.5 databases). They were all developed using a 5.0.12 designer.

Our names.nsf is ODS-43. My server copy personal mail database is ODS-43. My local copy personal mail database is ODS-41.

Apart from some apparently unrelated LEI issues (the problem is found in all databases that have agents, whether they are used in LEI activites or not), I note my automated agents no longer work.

A specific example: a database with a shared agent scheduled to run once per hour on all documents in that database where a field contains a particular value. When found, the agent performs two simple actions - Send Mail and Modify Field Value.

Until the upgrade everything worked like clockwork. However, since then the agent continues to run but nothing happens. The agent log contains this text:

Started running agent 'checkForUnmailedDocs' on date&time
Running on all documents in database: 999 total
ERROR: File does not exist

I've checked through the posts on this database and on the 6.x database and did not see anything, plus we are working with a contractor to help too. Any ideas or leads are appreciated.