GC 6890 will not start run after injection from CTC CombiPAL

I'm trying to bring an instrument on-line for eventual Headspace analysis. It is an Agilent 6890 GC / 5973 MS with a CTC CombiPAL autosampler. Apparently, last year (before I was hired) the CTC was installed by a 3rd party vendor, It works on its own, meaning it will perform all of its functions correctly, as controlled thru ChemStation. However, the GC run will not start after injection. The vendor exchanged cables, and even replaced a control board on the PAL, but they could never get the GC to start. They suggested that the GC Main board might be the issue. When I was hired, I was assigned to work on getting the instrument up and running. I replaced the Mainboard, and the issue persists. I do not think the issue is with the CombiPAL, but rather on the Agilent side. Unfortunately, no-one here really has any experience with this unit and can offer assistance (or a lot of background). Any assistance would be greatly appreciated. Thank you in advance. 

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