Are you up to date? I just checked and this behavior is gone on my machine. I'm pretty sure I know what you're talking about--disabling exoskeletons with the in-game controls makes your "slow" speed or the start of "accel" speed almost zero. But that was on an older version of the mod, not this one, before I refactored the core logic. You should be on 2.0.4.
If you are definitely on 2.0.4 and still getting this behavior, please upload your save file to dropbox or something so I can test for the bug more accurately and scan for mod conflicts.