I have been thinking about this problem that you are having and I think I know what it is... It is the acceleration that is your trouble but the more accel that you have the more you don't like the axis starting and stopping... it is not "smooth". If you take the derivative of acceleration it is known as "Jerk"... this is known as jerk because it is the change in the Rate of change... What the heck is that! you say... Well if you look at the graph of mach3's accel it would look like this:
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The vertical walls are telling us that we are getting very high Jerk and will get a shock into the machine when we start and stop a move. The worst would be to Reverse direction!
You would like to see an accel that looks like this:
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This will make for a move that will not give the sharp shock into the system.
Now for the bad news
there is nothing that we can do at this time to make this work for you... You need to have Scurve acceleration to get the jerk out of the system OR you need to have more mass to stop the shock (can't be stopped as fast, and is not a good fix). If you were running a Galil we could use the S curve accel in it to smooth out the accels in your table, but that would be about 1200.00 min to get set up
Just wanted to tell you where I think you are getting the problem from.
Brian