Mach3 just does as it's told and cannot be affected by mechanical issues as there is no feedback, it tells the steppers to move and assumes they have.
I use BobCad-CAM V25 and have no such issues so you can nail this down to what's happening before you get to Mach3.
Ideally someone who uses the same workflow prior to Mach3 as you will be able to assist,
Regards,
Nick