Tom,
The catch here is if one wants to use MSM, one needs the dev version of Mach3, so that leaves out the .032 and .033 and .040 lockdowns.
This is correct - the reason that MSM won't run on the lock down version as that it requires mach APIs that don't exist in the lock down rev.
Don't know what else to try until Dave chimes in with a tip or 2!!
Oh my, while I'm flattered, I fear the expectation may be more than I can meet in this case.

Here are some (maybe) relevant thoughts I've had:
There are three ways I can think of to get G-code into mach for execution.
1) load a file into mach.
MSM does this the same way all other screen sets do - call the mach interface to load a gcode file. A screen set has no knowledge of what's in a gcode file etc. User pushes button, mach interface called, mach returns, screen set's part is then all done.
2) MDI control
mach provides 1 MDI control - all screen sets use the same control. Again the screen set is not involved in the contents of the data entered via the MDI control.
3) Script Code statements. This is not applicable for the situation at hand.
Once ode is loaded, when the user starts the code, the screen set job is the same simple sequence of
a) button pushed, b) mach "run code" interface is called.
Again the screen set has no knowledge of a canned cycle - an conversion of a canned cycle is handled by mach and motion is passed to the motion device (at least that's my understanding).
So I'm at a loss for "tips" as to why you could see this with a MSM/SS combination.
Some other musings on my part:
1) Screens sets and plugins don't use any common interfaces that could conflict (MSM does not use a plugin to run). It was designed that way to avoid potential multiple plugin interface issues.
2) The PP driver does not interface to the rest of mach via a plugin interface - it is a more "intertwined" part of mach.
I suppose the combination you are seeing could be peck drilling via a plugin motion control device - but that still does not quite fit all of what you have described.
I can only do rudimentary SS testing as I don't have a SS connected to actually drive iron (just a bench test set up for the SS).
Right now, I think this remains an unsolved mystery until more clues are found by someone.
And (uh, no offense meant; really!) before going hunting, it would be nice if more than one person could confirm the problematic combination. Just to many unknown variables yet to make a plan of attack.
I will shoot Greg an email to ask him to read the thread in case he has any ideas.
Dave