Very interesting and well documented post.
Where were you attaching your scope probes and were they actual scope probes with individual earths?
I can't explain your first set of traces but the ones in your second probe look correct except have you got the cylinders/coils swapped round? Shouldn't the top coil in the pairs (1&2) show the primary above the 0V as its got the resistance (and therefore voltage drop) of the second coil to be included in its trace, where as the second coils in the pairs (4&3) are closer to ground (though same current flowing through both). Though you will never get 0V as you will always have the voltage drop across the junction of the coil driver (0.6V?) in there...
I guess it depends how each scope channel was earthed....but must admit my head is starting to hurt now trying to figure it out ;-)
Cheers
Sean
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