I have an assembly sketch that defines the lengths of a bunch of linkages. After I've created the motion study, if I then edit the master sketch within the model view, the changes will not update in the motion analysis. I have to repeat all edits in the motion analysis view. If I add a new part or add a new feature to existing parts (or even a new dimension to that assembly sketch), it will update in the motion analysis. Modifications to existing parts/features/sketches do not update.
Also, if I have a mate suppressed in the model view, but it is active in the motion study, it will be treated as active in the model view. My work around for this is to delete all mates from the motion study and create only local mates.
I'm running SW14 SP4.0