First I should say that the problem is now resolved. It was fixed after we cycled the power on the PXI system after attempting to download the "synchronize" option several times. The first time we cycled the power it did not fix the problem despite leaving the power off for >20 seconds, so the solution hardly seems reliable.
As for the evidence for lack of synchronization, initially we suspected a lack of synchronization as we observed "glitches" on the output of a digital phase-locked loop. The second clue was that the DPLL was actually locking to a slightly different frequency than it should have by about 5 ppm. All other FPGAs in the same PXI chassis were locking to the correct frequency.
We then wrote custom vi's that would cause one FPGA to generate a 40 MHz boolean on-off output on the digital front panel output. This was then looped to the FPGA under test (using the approporiate SCSI cable), which would read out the boolean at 40 MHz and register a missed count every time the boolean value did not change (exclusive-or between the current digital input and the previous input). Any given pair of FPGAs would give us zero unsynched counts, except when the suspect, unsynchronized one was used. The unsynched FPGA missed several thousand counts in a matter of seconds.
Notably, we had this problem with 2 different FPGAs in 2 different PXI chassis. In one case it was the 7833 that was the problem and the 7813 worked fine. In the other system a (different) 7813 was the problem and the 7833 synched fine. We have two more FPGAs waiting to be installed and I will post back here if I see any more issues. We also have three 7811s and three 7831 none of which had synch problems.
Once the synchronization problem was fixed it has not reappeared again which is good news for us.
Thanks,
Daniel