I use AC 1.2.1 for iPads at one location, and I just started using AC 1.3 on a different MacBook Pro to deploy 1,000 more iPads at a different location. I am only using three iPads at that location for testing for now, and I have noticed that AC 1.3 does crash often. I think it has something to do with applying multiple updates to All Devices without plugging each device in to let it finish the first updated applied - that is just a theory. Regardless of what is causing the crash, once AC crashes, it crashes every time I restart it, even after rebooting the MacBook, until I disconnect all iPads, restart AC and "stop" the pending updates. Then, I reconnect one of the iPads, and it does not crash again until some combination of applied updates.
That said, is it possible that you have updates "pending" from the original AC 1.2.1 installation - I think those were shown as "Waiting to Connect" in 1.2.1? Can you stop those by clicking the Stop button in 1.3? I thought of that because my first AC 1.2.1 shows the status of "Waiting to Connect" for several iPads, and I thought AC 1.3 was suppose to fix that with the Stop feature. (This is slightly different, but I had random iPads crashing when I plugged them in to AC 1.2.1, and I am almost certain it had something to do with the "Waiting to Connect" status. Have you noticed that problem too?)
I hope this helps, and I hope someone has additional thoughts on this.