Pretty sure you will have the motor tuning set wrong. First off the settings are not in cm but mm and motor tuning is set in steps per mm.

To work out your Steps per millimeter take the Micro stepping value set on the drives and divide by the ball screw pitch. If you have any ratio applied you'll need to take this into account. So lets say you have drives set at 800Ms and 4mm pitch screw with 2:1 ratio. The affective pitch will now be 2mm for one revolution of motor. So Steps per MM = 800/2=400

Velocity is set in MM/Min and how you set this will be dependant on several factors. If your just using the parallel port then you could be limited by the Kernal speed depeding on drive settings, pitch etc.
For instance 25Khz kernal speed with drives set at 1600Ms will give maximum motor RPM of 937rpm which with 2mm pitch gives Max velocity of 1875mm/min. Works out like this. 25,000 pulse per sec /1600Ms = 15.625 rev per sec so 15.625 * 60 sec= 937rpm * 2 (mm)=1875mm/min

Now this is the maximum and in real world use you'll be down more towards 1500mm/min for a stable machine.
So if you have actually set velocity to 350cm min which is 3500mm/min then as you can see this would cause stalling motors when speed increases.

If you have set it to 350mm/min and the steps Per setting is correct then you probably have other issues like binding axis etc.?