This sounds potentially dangerous:
"For whatever reason when I try to run a program my machine will just stop and not move unless it decides to start going again or I restart the program"
Has the program you are trying to run been run successfully before?
When you run it and it stops, does it stop at the same place or is it different each time?
Does the machine function properly using manual control (Jogging from the control panel, Pendant or MDI)? If not then some troubleshooting might be in order before trying to run programs.