I think You're on to the right answer...

HCL Notes/Domino 8.5 Forum (includes Notes Traveler)

Subject:

Yes - I believe so. According to what You are describing it is most likely the case that the COM object handle isn't released in time for the kill-command to execute.
If the COM API for the 3rd party tool is somewhat similar to Word/Excel COM, then there should be a command for save, a command for quitting the application (and thus releasing the handle to the file). If not - then You're in trouble.

Try to see if the handle is automatically released when the agent quits; Try this by having ANOTHER agent run that only has the job to delete the file. If that's ok - then it is a handle-release problem.

hth

Feedback response number WEBB8LWMAM created by ~Vanessa Preponelyynds on 09/21/2011