Hi Randy,
I ran into this exact same issue a couple of months ago.  I set up my system so that I could test the CJC temperature by making a really long thermocouple and then using a heat source pointed directly at the connections on my SCXI-1328 terminal block.  I noticed that all of the TC channels seemed to be moving even though the the actual TC was not changing temperature.
What I found the problem to be was actually with the way I was doing my testing.  When doing my testing I was actually heating up the area where the signals were connected at a different rate than the CJC Circuitry.  When I tried a methodology that provided for a more even heating of the Terminal Block, then my problem was eliminated.
There is a good KnowledgeBase that explains this behavior call 
Why Am I Getting Temperature Drift on My Thermocouples When My Cold Junction Temperature Changes?.  You can also find it by going to ni.com and searching for 'temperature drift cjc'.
As far as your programming is concerned I'm sure you have that part right.  I usually like to test things in MAX to make sure that everything is working right, then program it out in my .NET code.
Best of luck getting the rest of your system together!