if your loosing boost, check all your vacuum lines, cooler pipes and the BOV, if its a HKS replica its obviously cheap shit and quite possibly leaking boost.
get rid of the GFB boost controller and hook up your standard solenoid (if you have one) that should run 7psi on highboost and if it doesnt piss around and carry on then you know the valve is bollocksed (which wouldnt be hard do believe)
also, remember the standard ECU has a boost cut, if your running a squillion pounds on your standard tune the engine WILL stop it from boosting, mainly to protect the engine. ALSO! you have a standard AFR.
so your fuel/air ratios are not tuned and the more boost you run with a standard setting the more its not going to like it.
basically it could be anything. just have a look at all that.