OK, I am running a new part program and whnever I start a new cutter I deactivate limikts foir a short while because until I break in teh cutter I get a lot of whinning/vibration and that sets them off.  Now I got a new problem, After I deactivated limits and teh program got to the parts where G41 is called up teh first X move occurs in teh worng direction.  What is teh connection between limit switches being deactivated and the direction pin?  Anyone else have this. 

I also have this other problem where after about 200 parts in teh same program I get suddenly halted rapids and cutting begins in the wrong place or a move doesn't get executed.  This occurs about 1/40 of the time sometimes followed by a SS halted message.