Haven't figured out how to cause the bug as it seems to happen somewhat randomly. Quite simply - the ship flies backwards, as if holding down 's' when no buttons are pressed. This can be countered by pressing 'w', and the ship then flies forward. This persists across maps - restarting a map does not fix the bug, but restarting the game does. This might have to do with alt-tabbing, however I cannot reliably reproduce this.

Does this happen to anyone else?

Start a new profile without copying controls. Then try it.

Well, in the sort time I played with the other profile, I wasn't able to reproduce the bug.
However, when back in my main profile the bug occured again, it persisted after changing the profile.

Due to the nature of the bug, it may be quite difficult to just keep playing till it happens on the new profile. Will keep trying.