Polarity on the pick-up wiring was my issue when this happened on a 360 with a MSD (I know you said you already checked this). What about the wiring itself? Unplug it at both ends and check both leads for a short between them and check both against body ground as well.
Next thing I would try is a known good ignition/coil/distributor wiring it up completely with new wire isolated from the existing.
I had a complete 2nd summitvdigita system wired to nothing but the battery direct and ran it with my msd distributor with leads both ways, and a summit msd knock off distributor, also, wired both ways, the summit ignition I borrowed had another brand new set of leads, I used those on both ignitions when testing the supposed correct polarity on both distributors and both ignition boxes, I cut my leads and put connectors in the middle so I could reverse them.
Odd question.....AM I IN NEED OF ANOTHER GROUND WIRE?
