TT are you saying the inlet valve is open when the plugs ignite the fuel/air mixture?
I'm not saying that yet. I'm just stating the root physics/chemistry requirement. I think that's a first step toward understanding the issue.
I don't know your cam specs as to when the intake valve is supposed to close with respect to BDC. (could be on part of the compression stroke which could push some fresh charge back into intake runner at very low RPMS.
I don't know what your spark ignition timing is with respect to TDC (or if it is set *to* specification.) This can be BTDC and if there is intake valve leakage, fire gets to the intake runner. I also don't know if you have some spark energy cross coupling between spark leads, so that spark can occur near BTDC.
I don't know if there is an ember in the intake runner.
I don't know if your valves are sealing properly.
I don't know if there is cam lobe overlap where the intake valve may open during the exhaust stoke, pushing some unburnt air fuel mix into the intake runner. Then, due to the wasted spark system, the plugs fire between the exhaust and intake stroke, igniting the ripe mixture.
This later possibility seems the most likely on an engine in otherwise good health. But, there are lots of things I don't know.
So, what are your cam specs, and is your spark timed correctly? What is that spark timing relative to the valves and piston positions?
Cheers,
P.S. Remember, no one has given me a 650 to play with, yet.