Hi,
I'm not sure what you re seeing - so I'll do some guessing to see if any of this rings a bell for you...
1) keyboard input for joging is handled directly my mach, so I'd expect any symptom should be the same whether you are running MSM or not.
2) Assuming that you are doing step jogging, what jog mode is being used? V, S/V, S, or M?
From memory. I think S should give you one unit of distance as set in the DRO to the right of the STEP button.
However, if you hold down the arrow key. the PC will cause the key to repeat - and that will buffer up multiple job increments in the PC keyboard buffer. Coupled with a large step increment, this could result in a lot of movement after the job key is let up. Could this be what you are seeing?
3) for keyboard jogging my usual jog habits are to use cont jogging - that gets me close to where I want to be, then If I'm using the keyboard, I switch to Step and S and only hit the key once per movement. (sort of a "Dr it hurts when I do this... so don't do it" approach

)
4) the jogging stuff works in a sim installation (at least with the PP), so that is a safe way to experiment to see how much movement occurs after a jog key is let up using the different combination of jog modes.
Dave