Hi, Clint
In motor tuning set the Step&Dir Pulse's to 5, This will give your stepper control more time to see the Pulse's
Setting up Vel. & Accl. is a balancing Act !!, It's primarily used for Rapid Moves (G00) Your F?? set's your Cut Speed's and will override Vel./Accl.
Set the Vel. Up to a speed that it start's lousing steps then back it down by about 10%, Do the same process for the Accl.
Use a distance that will allow you to see the top Vel. and then return to a stopped condition, G00 moves.
I think your accl. may be set to low.
Have you run the Driver Test, It's located in C:\Mach3 Folder, Run it and see what it shows.
If you have large spikes in the graph you may need to clear up Windows.
Thanks, Chip