Register Test Intermittent failures

We are in the very early stages of product development and are using the Myriad and Zipper combo of boards. We are using the Lms-suite software for configuration and it has a register test the fails about 10-20% of the time. So far we have been unsuccessful in capturing the failure on a scope or logic analyzer to so not know if it is hardware or software. We have two boards and both act the exact same way. Has anyone else had this problem?

The failure seems to be always when the ATMEL chip sends a long packets of data to the LMS6002 and never during a single register read or write.

Any help or suggestion would be greatly appreciated.