Thanks Brad, I'm afraid I don't use adPro or DiskMaster2 so can't test them on my setup, maybe someone else can.
Unless a program (whether an application or game etc) opens on a window in Workbench, automatically open in the same resolution as Workbench, or has its own prefs where you can choose the resolution, it will default back to using the native RBG output. It can't be forced to open via RTG. This is a limitation of the program, not of the video driver or PiStorm.
I've seen things on twitter etc about a video passthru from RGB into Pistorm which is in development, but I think this involves hardware too. I'm not sure.