Just to finish this thread off....

Ended up calling Beaky (thanks heaps mate) and talked through a few things, double checked EOS, all fine, and found that when earthing the middle lug of the coil it was still relatively weak - since i had swapped the fliptronics board to a known good one, it pointed down the coil end.  Sw i swapped the flipper coils over (the weak upper one) and it came all good.  Now i can't say for certain, but i'm farily sure it was a mechanical issue - even though i had checked it a few times, when i gave it a good look, there was some light wear marks at the end of the plunger - near the link.  So even though it seems to have moved freely without resistance, there may have been just enough to cause trouble??? I did remove the coil stop bolts and re-align them - its possible these may have been slightly out of kilter making the coil a bit cockeyed. 

The lower flipper that was getting hot was the result of the owner losing the small bush that goes in the plastic link at the end of the plunger - this introduced a whole heap of slop into the ssytem, that really only became evident when you pulled it apart.

So all sorted now, thanks again Beaky for the pointers over the phone