I was just about to ask for the motion instructions info. Glad you posted it.
For the moves the profile type is set to "trapeziodal". This means that the jerk value in the motion instruction and the jerk limit value in the axis configuration don't come into play.
When you look at the axis set-up values you can kind of get a feel for where they come from by the significant digits that are displayed. For example, in the Dynamics tab in the comparison document you provided the max speed, accel and decel values have no digits to the right of the decimal point for Wrapper 1.
For Wrapper 2 there are several. This tends to indicate that someone typed in the numbers for Wrapper 1 and the values for Wrapper 2 were calculated in the development software. The problem is the accel value is based on the inertia values from the Output tab. Wrapper 1 has a load inertia ratio that looks pretty reasonable. Wrapper 2 does not. So while the values for Wrapper 2 Dynamics look more reasonable, those values appear to be based on incorrect information.
So if we assume the Wrapper 1 inertia numbers are right and the resulting Wrapper 2 accel rate is right, the true physical accel limit is probably around 3100 in/sec^2.
The programmed accel rates are 2000 in/sec^2 for close and 3000 in/sec^2 for open. That is definitely aggressive, especially for an axis with a trapezoidal profile. I assume the recipes are the same between both wrappers? As for the MAS, it looks like the instruction is changing the the accel rate to 10% of the limit value (340 in/sec^2 for Wrapper 1 and 520 in/sec^2-ish for Wrapper 2) and the jerk value to 100% of the accel time. This is more gentle than the MAM parameters by a fairly large margin so I don't know why this would be done for an abort, but that is what the instruction says.
Another thing I notices in the axis config compare document is that Wrapper 2 has velocity feed forward set to 100% while Wrapper 1 is set to 0. I would think this would cause some position lag in Wrapper 1 that is not present in Wrapper 2. In addition, neither of them is using any acceleration feed forward. With accelerations as aggressive as those set here I would think accel feed forward would be a big help. More so with Wrapper 1 than Wrapper 2 since I think Wrapper 2 total inertia is closer to correct. But it would help both.
Again, what is the failure mode of the ballscrew systems? Are you tearing the ball races out of the nuts, tearing the ball tracks off the screws or twisting the screws in half?
Keith