Your device must be configured for non-referenced single ended when using SCC signal conditioning hardware. This is why you are getting incorrect readings when configured in differential mode. The document linked below discusses this. I hope this helps.
What Grounding Mode Should I Select When Using the SC-2345 Carrier for SCC Modules?
http://digital.ni.com/public.nsf/websearch/A838F826A32752E786256B1200646776?OpenDocument
Regards,
Todd D.