I don't know this engine well enough to comment knowledgeably, but are you sure it doesn't have a pick-up span near 6" from the extremes of its pick-up base? If two good pickups, one on each rail, are separated by even 3", then you have other issues, probably with the integrity of the turnout. A 3" separation will extend well beyond all but #14 turnout and higher dead frogs. So, I am inclined to doubt that the engine is the problem, unless it is actually defective in terms of solders between pickup and motor/board or decoder. But some turnouts can not transmit power up their points rails because of poor contact or defective wipers below the points if they are supposed to work that way.
I would place a high premium on the use of a multimeter in this situation, first on the engine and then on the turnout. Then, if both check out, meter the turnout once the engine stalls on it.
Crandell