Doug,
The following two threads may help point you in the right direction. My first thought is that you are running into an error I saw last year regarding a bug in the wire library where when you issue a read command, the Arduino outputs a STOP in between the write (register address) and the read portion of the transaction. More detail can be found in the first thread along with a work around. However, from what I recall, this problem did not hang the cRIO, it just returned a transaction failure, so your issue may be different. Let me know if this helps. Also, if you can post your code, I could take a closer look.
Mike
Link1
Link2