You need basic invetigation techniques here. On something that has worked a long time, then broke, I asked what changed recently? When the operator (may be you) says it can't be that, I think "Oh yes, it can".
You've got to have a bunch of new code in your .cbk for that touch screen. Before even starting it sure sounds to me like DECELSTOP is in effect. I'd search a log file for this command.
If you don't find it with one or two quick guesses, start by dividing the big problem into two smaller ones. For example load a default .cbk that you used when you first got the machine and only change your PID settings. Does the machine perform correctly regarding this issue? If yes, you know its in the .cbk somehow. If no, look to hardware or Galil programming. Keep narrowing down till you find it.