The commit that introduced the stop is 303a920. I vaguely recall the change being a workaround for less-than-idea behavior of a motor controller, but neither @rsluiter nor I remember which controller that was.
Motor drivers should be modified to send the stop command when the condition that triggers the setting of the problem bit is detected, if needed.
Partially reverts commit 303a9208e368ef07839afff67bac69e429af7332
Fixes issue #100: