Assuming that your carburation is standard (jets, needles, float level) and working well,
and assuming your PGM is OK,...
... all I can think of (and it is a total wild guess, long-shot) is that maybe the variable resistor in the Throttle Position Sensor on the carb is giving trouble or is wired up backwards?
I do not know what the PGM does in terms of ignition timing in relation to throttle position, but I imagine that it probably retards the spark a bit if it thinks the throttle is near closed?
I assume you are only using small amounts of throttle when the bike is on the stand, as opposed to large amounts of throttle when out on the road???
I'll keep thinking about it anyway.
Also, check the front brake isn't on!! Just kidding.
