Years ago I had a problem with thermocouples right about when the first TC card for the SLC 500 came out.
Ironically it was a project I did for an OEM for Allen-Bradley at their main HQ in Milwaukee. To get the answer, we called the engineer who designed the card who was within that building (now that's service!).
He determined that the thermocouple was unshielded and needed to be shielded (or vice versa - it's been a while). Anyway, getting the proper TC fixed the problem. However, that was back then using a different card. If the card you ARE using is a 1746-NT8, it supports either grounded or un-grounded TC's, so be sure to wire them up as the manual shows. (I just checked A-B's website about this.)
For the record, I also agree that it could be a configuration problem...