With what you said "The only way to run the workflow is to right-click on the workflow and select reset from the menu" it would seem the cache history is enable. That's means each time your file is processed, FFAStrans "remembers" the file. You can avoid this : check "forget missing file" in Monitor folder to help FFAStrans to "forget"the file.
Please let us know if it is ok
Yes and you MUST enable it if you want FFAStrans forgets your file once processed
So, check "forget missing file", reset your workflow once and it would be ok.
Cheers.