Yep both connected to the PC, 2 ports directly next to each other. Also correct, just the MTE leads.
The next day I did try connecting the differential reference lead to the input lead with nothing else connected and still getting the 30V spikes.
Also, if I am remembering correctly, there used to be a clicking sound when starting the scope, like mechanical relays. I no longer hear that when starting the scope instrument.
I will try connecting the AWG to the scope input in the morning.
Update:
I just tried on another PC, and it worked, so I switched back to the original PC, and still had the same issue.
I then switched to the USB 3.0 port, and it worked fine in that port. Switched back to the original port and the issue returned.
Not sure if it's the data rate, or a power issue, but for now everything is working on the USB 3.0 port.
Thanks for the help!