Before you flash the AutoShift example firmware, you’ll need to clear the EEPROM first. You can do this with the “factory reset” in Chrysalis. If you don’t, AutoShiftConfig will attempt to read configuration data from what is essentially a random location in EEPROM. Alternatively, you could comment out the AutoShiftConfig plugin from the example sketch.
That’s very surprising behaviour. I have no idea what could be causing it, frankly, but it’s not really a valid test, because you’re getting pseudo-random config data for AutoShift.
I’ve been compiling sketches using Kaleidoscope master, and the AutoShift example has only exhibited problems when the EEPROM on my Model01 was configured for a different set of plugins.