[Alan Anderson]

But was the BAT light on?

Seriously, everything you've described (excepting the pneumatic leaks) points to the Digital Sidecar not getting battery voltage to its power input. It'll get a tiny bit of leakage through the ribbon cable from the DIO module that makes things seem to work, but everything will quickly get flaky, especially if you have only a few motors defined or try to run more than a couple of them in reverse at the same time.