OZ, I did not ever have a issue with the manual runs, I could not create the same tables.
SOOOO....
I completely deleted everything, cleaned registry both with jvtools and regedit.
re-installed everything and ran transportation today and everything is fine. Ended up with the MP_TYPE needed to go forward but interesting it took twice as long (7 hours) and file is twice as large.
One thing I did was to attempt to do things one stage at a time, ie: download, then come back and combine, then comeback and process the current set up only allows combine at once, no return to operation.
But what the hey it is a great tool even if I had some issues getting it to work.