Is this a new problem or has it always been like this?
I have never come across this problem but I guess it could be due to any number of things?
I will just assume that the PGM is working well and the power valves are set properly, although you may want to check these.

Blown base gasket or head gasket
Crank centre seal
Check compression is approx 140 psi on both cylinders

Check airbox and filter flow air freely
Check reeds
Check pipes flow air freely
Check that fuel flows freely into the carbs from the tank and that the tank breather works.
Check that the flywheel spins true and cannot move (up/down/forward/back) due to worn main bearings. This may result in sporadic pick-up sensing?

Umm, that's all I can add for now.
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