Hello Brian,
1. Machine Coord DRO's don't always zero they will have 0.0013 left in them sometimes.
I think you are setting zero with the Reff command with no home switches .. This is a known problem at this time (I will fix it but it is working with home switches). Also if you are going to set zero you should use the Zero x,y,z buttons... Last what is your steps per unit ?? You may not be able to get to zero (Limitation of your machine) and this is as close as the software can make your machine round the digital steps to zero.
2. Step and Dir pulse lengths on some installs will reduce upon opening and closing the motor tuning window.
ie. Step=2 Dir=1 after opening, setting, closing , opening motor tuning will change each by -1
This is fixed in 3.042.015
3. Program extrema is not being calculated correctly.
Could you please give an example of what is not correct? For example are you running loops with offset shifts and so on in the code? If so it is hard to tell if you are in the correct position when the reference position is changing

That is the only time that I know when this is not correct..
4. Mach seems to be having issues saving CV state if you change the CV dist tolerence or turn CV dist on/off.
Closing and opening the session fixes it, but I've learned mid session changes are risky behavior.
You should close and reopen the software to back up your settings...This is a very good idea
5.Mach is parses the code pretty slow when you open a file. I'm guessing it parses the code for gcode errors and finds program extrema.
I would like to be able to turn off the program extrema calculation method or see it rewritten using RegEX so that it parses faster.
It is also the calcs for drawing the toolpath that is slowing down the load time... In the diagnostics page please turn off the toolpath and tell me if you like that better.
6. If you jog the machine during tool change M6 (so as to be able to physically get to you spindle and change the tool upon pressing cycle
start mach moves to its previous position with no warning or way to cancel this. This needs to have the same dialog added that you get when using
"run from here".
Please have a look at the M6Start.m1s and M6End.m1s macros and change them to your liking

This is the only way to change how the toolchanges are done
7. Machine is always underfeeding. If I set feed rate to 100mm/min and give the machine plenty of room to make a single axis move and get up to speed
it is always under feeding by about 4mm/min, it never reaches the programmed feedrate and my max velocity is 800mm/min. It didn't do this in older mach versions.
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This has to do with how the feedrate is now calculated.. in the end are not far off (less then one %) this has to do with the amount that your CPU timing is off from what it should be...
Hope that helps you
Brian