I'd have to go back and look at your ignition setup, but I'm in the process of familiarizing myself with the MSD 6AL box I'll be installing (eventually) on my car and it mentions engine run on, similar to your situation when using the MSD box with a GM HEI distributor. Basically describes that there is some sort of signal that must be bypassed, otherwise the MSD box continues providing spark. Kinda leading me to just do my engine break in without the 6AL and wire it in afterwards.
Never know, but it might be a good place to start your gremlin hunt.
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- Peter -- 66 Le Mans - 93 LX 5.0 --
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