Yes, it would be a decent idea to load up the default method (like def_gc.M) and default sequence (def_gc.s) make minimum changes and see what happens.
Any error message on the monitor when this happens? How long do you wait until you "punt" when this happens? I've noticed on mine that if I load a Method that has low temperatures for (example) the front inlet, front detector, or aux, and I only have a column in back or only using the back location, EVEN IF THE FRONT ZONES AND AUX ZONES ARE UNCHECKED under "Temperature", the GC will not become "Ready" until those zones drop to whatever temperature they are set for (even though "unchecked"). Go to the "Temperature" window when this happens, click on the other location inlet and detector temperatures, and aux, and see what number is entered there. If low (or high), make those maybe 125C, then click OK. Then go back in and just remove the check marks for those, click OK, then re-save the Method. I had to do just that yesterday when setting up one of my GCs to do parabens, which I hadn't done by GC in years; mine was waiting for cool down of the aux zone, even though I wasn't even using aux, it was just carried over from a previous Method I started with.