The difference between them is: The 3601 box is HD and the 4000 is SD.
The shows come in on the Pathfire as SD but 16:9 and are being played out to air on the 3601 in 4:3. I tend to think that when the file is flipped from the Pathfire catch server to the Nexio, the CC is being garbled then. If I do a base band recording from the Pathfire to the Nexio, bypassing the flipfactory completely, and then have the Master Control Operator go in and segment the show like it was dumped into the Nexio from tape, the CC is fine. But we shouldn't have to do that. It should work and so far neither Pathfire nor Leitch (the makers of the Nexio server) are willing to admit that the problem could even possibly be in their stuff.