Hi Guys,
Dusty contacted me about this topic on the CVI support forum forum - I thought I'd offer an update.
I suspect the root problem was with Mach 3.43.22 and PP driver 570 (which is what Dusty tells me he had running when he experienced this issue).
For MSM use, we recommend mach 3.43.37 (which also installs PP driver 601). I've settled on mach 3.43.37 as the MSM recommendation as it has patches for some serious safety issues that exist with the lockdown (3.43.22) rev.
(BTW, if you want mach 3.43.37, it is avail (via permission) from the CVI web site download area at
www.CalyopsoVentures.com since it is not on the FTP page of Machsupport.com)
It looks as if the index pulse problem exists with the PP 570 level driver but is fixed in the 601 level driver.
I have some hints as to what the internal issue is in the 570 PP driver from correspondence with Art, and it involves changes in how plug-ins and the PP driver interact wrt to updating the RPM DRO (39) - I suspect the change Art made for that also fixed whatever this issue is in the 570 PP driver re threading sync (as there is only one input pin for the index pulse, the driver does both the RPM DRO update and Threading sync handling).
In any case, whatever the mach bug is, it seems not to exist with mach 3.43.37 and PP driver 601. I did not go back and verify the bug on 3.43.22 and driver 570 (as that would have required time that I didn't want to spend just to verify a mach bug).
FYI - to test this I set up a test system, connected to a PMDX125 breakout board on my test bench. It is fully configured for 3 axes and I'm using a signal generator to supply index pulses to the BoB - so I know it's getting nice square 50% duty cycle index pulses and I can vary the pulse speed to anything needed. Essentially this is a complete PP control system that just is not hooked to motor drivers (though the motor tunings etc are all configured).
I then set up 3 mach profiles, the only difference between the three are the profile names and the screen set the profile loads.
The first profile loads the mach 1024.set screen and gives stock mach mill mode.
The second profile loads the mach 1024.lset screen and gives stock mach lathe mode.
The third profile loads MSM.
I've used the test set up to run mach with 1024 mill, mach with 1024 lathe and mach with MSM, shifting from one to the other in all possible combinations. I can do that and I can run the threading test gcode (that Dusty said failed for him) every time without problem. I've also not had any trouble running any other gocde with any of the profiles - so the "proof by example that it's possible" is not dependent on the single gcode test case. I think that verifies that it is indeed possible to run MSM and mach lathe on the same PC without needing to uninstall MSM and reinstall Mach to make a lathe work.
So to set the record straight for those that may find this thread in the future, while using MSM may have illuminated the situation, the root issue is not an MSM bug, it is a mach bug.

Finally, from a post he made on the MSM forum, I have the impression that Dusty has this solved too - I've pinged him to verify that and am currently awaiting an ack that the mach update resolved this for him too.
Dave