Have you tried reversing the leads from the MSD box to the distributor? If the polarity to the distributor is wrong, it will require the advance you are talking about to run, but it will never run good reversed.
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.