I can't speak to how things should operate for a grnd checkout, but a GTC issue has no bearing on your original problem. I have been battling a very similar issue for the past 2 weeks in flight, and after a CND, an r2 press cont, an r2 outflow valve, MX has finally taken my advice and looked at the aux vent valves. The CC aux vent valve was intermittent, and must have been cycling closed and not-so-closed in flight, which led to a fun sortie with me recycling the outflow valve every 5 min or so to battle the climb/descent rates as the aux vent valve changed position. I've also had them simply stick, which means no flux, but a much lower max in/hg differential.
My advice is the same as keepemflying's, check em out, hope it works for ya.