The only thing sure, is that it wasn't related to GSX in any way. GSX fps impact is hardy noticeable in the outside view, when you see all the vehicles at once, but it's really zero in the VC, because FSX culls everything that is not directly on sight so, you wouldn't see much of GSX vehicles.
And, since GSX logic is entirely external to FSX, because it runs inside the Couatl interpreter, there's no way GSX could slow down FSX with its own processing.
However, if you search around, there's plenty of reports of issue with low fps with the NGX in VC, and there's seems to be an interaction with the mouse cursor position, for example here:
http://forum.avsim.net/topic/341886-fps-drop-when-mouse-cursor-visible/