New Software Issue with Cut Control

I was running a program this morning and had some issues. First issue was when I selected the forth operation and hit cycle start the software went to the fifth operation and cause a crash , which I was able to stop before major damage to the part was done. I rebooted everything and reloaded the programs, everything ran fine until the last operation (10th). Now the machine keeps hitting the soft limit switch when I hit cycle start and requires it to be homed. Rebooted the machine again , replaced the limit switch on Z axis, reset the soft limits , still same error. Any ideas. Sending ticket to Jake.