I don't have many ideas yet.
I recommend not trying to update or recover on the robot. Remove the Jaguars and update them as the only one in the chain or the second of two in the chain (the case where you use a working Black Jag as a bridge).
You said everything seems to be working now; you you have an issue with that specific Jaguar again, don't hesitate to go through the RMA process on
www.luminarymicro.com/jaguar.
Some troubleshooting tips:
If many Jaguars are exhibiting the problem in many locations on the bus; double check that you're updating things correctly and your code written correctly. Check your cabling and check for metal shavings that may have worked their way into the modules (don't back out the screws on Gray Jags!).
If (many) Jaguars act weird only in a specific location on the bus; double check the cabling and make sure that that specific Jag is being coded correctly. Also check for metal shavings!
If only one Jaguar has acted weird; double check all of the above but if ALL else fails, consider filling out an RMA request. You'll answer questions, and work with our support team to determine if we can replace your unit.
I hope ship day went well, good luck at your regional!
-David