The in-game sensitivity appears to revert to default each time the game is run. This, however, is not reflected by the in-game sensitivity option, and subsequent changes to the in-game sensitivity do not appear to do much. Fiddling with the sensitivity and window size seem to eventually resolve the issue for the running game instance, but I have been unable to create a reproducible method of fixing it.
This appears to only affect KB/M controls, as controller input is very consistent.
This appears to be fixed in version 1.1. I will continue to test to see if the issue creeps up again.