I took the y drive plug out of the controller and swapped it with the Z plug on the front of the control box and then jogged z using what would normally be the y quick keys. problem didnt occur in z but does now appear in y. I didnt physically shift any wires inside 
This proves that the motors were working correctly for both axes, so no need to upgrade those.
The problem occurs between the computer and the controller output.
Based on this it could be the controller board, PC port, or the software (including a software configuration error).
The fact that they state their preferred software works is significant - they probably also provide a config file which sets all the correct software config states up for their machine to operate
x axis is active low, other 2 arent.
X axis pin 2 direction 5v
X axis pin 3 step 5v
Y axis pin 4 direction 5v
Y axis pin 5 step 5v
Z axis pin 6 direction 5v
Z axis pin 7 step 0v ??
Very confusing.
I am wondering if you have mistyped something, and that x & y are active low, and z isn't.
That would make more sense.
If that is the case, try changing the sense for the z axis step control.
Other thing from left field, is the PC doing something after 5 or 10 mins?
eg maybe a memory cleanup 'garbage collection' cycle or swap file flush etc.
I had a similar problem when I first set up my machine.
Trying to mill a test piece it would skip on the z axis at about the same place everytime (the 3D face test file, doing the fine cut about 5 mm into the side about level with the nose)
I finally fixed this by removing the ACPI chip driver and replacing it with the 'Standard PC' driver.
I presume some long delay interrupt triggers or similar, and windows gets sidetracked too long to drive the motors properly.
Now I have replaced the drivers, the machine has never skipped since.