I've run the Q/S 2 different ways on my Gen II through the ECU and have not a problem that was not self induced for several years no F1 light.
There are 2 methods of doing it. One is to use a resistor in the switch wiring that plugs into the gps harness then program for resistor in the ECU like a Gen I. Downfall is you can't change kill times or be gear based etc. Or just run a switch into the DSM circuit with one side to ground and program either DSM1 or DSM2 in the quickshift portion of the ECU. I use my horn button when I'm racing production classes. Now here comes the WTF part. Woolich has decided in his most recent software, that automatically updates, to get rid of the Q/S option unless you buy his shifter with the "race tool$" package. Unless you have an older file saved that has the Q/S button you may be SOL. Since I have saved some of my old files I haven't had to deal with it and there may be a way around it if you are not using a foot shifter, I don't know.