When is it not cutting through, and what error are you receiving on the Height Control?
If you cut out a single one repeatedly with no errors, I have a few suggestions of things to look for.
Make sure that your nest isn't too close and attempting to pierce over an existing hole. Make sure that your air supply for the Plasma cutter can keep up with continuous use. Make sure that you are checking the consumables for failure regularly.
With a little more information I can help narrow this done further.