You might want to check out the FRC Diagnostic Window app from WPI's Think Tank. It's a very useful tool for "directly" twiddling outputs from the DSC and reading analog inputs. If you're suspicious of your hardware setup and don't want to separate SW issues from HW issues, this app at least gives you a (hopefully) solid SW app to start with.
http://thinktank.wpi.edu/article/138
If I'm understanding your description (I don't have the bandwidth to download the pix right now), why are you moving the digital I/O module from the cRIO and using a 15 pin serial cable instead of keeping the module in the cRIO chassis and using a 37 pin cable? Interesting design choice... Maybe trying to save a little weight?
Have you confirmed that your 15 pin cable passes all 15 signals straight through instead of swapping pairs of signals? I'm not familiar with any 15 pin serial cables but there are certainly 9 and 25 pin serial cables in both straight and crossover configurations.
Also, there are (I believe) 20 or 40MHz SPI signals going from the cRIO chassis to the digital IO module. Passing those signals through a long 15 pin serial cable could be problematic. You may be getting inadequate comm through that cable.
Good Luck!
Russ