I always design mine for 100% open but as Charles Lamont stated yours should work perfectly well if properly timed.
When you stated that each cylinder runs perfectly well on its own - that begs a really daft question :- When you run them on their own are they running in the same direction ?
If not they are "fighting" each other.
Perhaps the more efficient cylinder dominates occasionally and it runs but roughly - it would also explain the apparently frictionless knocking.
My apologies but I had to ask.
Another diagnostic you can try is to hold the engine stationary by hand - apply pressure - then turning the flywheel by hand diagnose where the pushing and pulling occurs as well as any bypass, leakage or any other inappropriate flows.
Is your "D" valve sealing against its running face - are they both perfectly flat - show us a photo of the running surfaces.
Regards, Ken