I'm not familiar with the MSD stuff, but something along those lines makes sense. This is the reason I advocate getting rid of all the "hi tech" ignition and putting a basic points system in until it gets sorted out.
You post sounds like that you are basically saying "its a rotor phasing problem."
This can happen in many systems, especially with "non factory" wiring, whereby the trigger that makes the spark happen (reluctor/ trigger wheel) does not make the spark when the distributor rotor is aligned with the distributor cap plug tower contact.
