I am getting messages that either say RADIUS TO END OF ARC DIFFERS FROM RADIUS TO START. ALSO IT SAYS TOO SLOW FOR PULLEY USING MIN. 
looking for suggestions that may help. I have a Galil motion control. I design on FLEXI and get my G CODE from ENROUTE

"Too slow for pulley" means you are commanding a spindle speed lower than the minimum set pulley speed. If the speed is what you want, change the min pulley speed to a lower value.

Radiud to end of arc usually means you have programmed in incremental IJ, and have Mach set to absolute IJ, or the other way around.

So when I try to cut a square for example the program will lose its place and then somehow finds it way back? could this be a problem with the motion control?

I already gave them to you.

goto Settings and check witch pulley is selected

goto Config -> Spindle Pulleys and check Min value of selected pulley

for radius Problem goto Config -> General Config and make Setting correspondig to post processor