Gina,
Here are 2 hypothesis that you could validate:
Hypothesis #1: The As400 docs system ignores the dot '.' in the filename.
To test this, you could try sending a dummy pdf named something like 'A.B.C.pdf' and see if the archived file has the same name.
Hypothesis #2: The Workflow variables are not instanciated properly.
To test this, you could try your actual process with the file name changed to something like '%f.pdf' and see if the archived file has a name like 'job123abcwercwec.pdf'.
Hope this helps!
Feel free to post your results here.
Benoit