O.K., Technobabble aside, I thought ALL BL timing was in the controller too, however the more I read the more it seems there is some 'timing' built into the can as well, (and wye is very sensitive to it (I'm assuming)).
The only thing I could think of as 'directional' (or 'timing') in any way would be the direction of the current in the stators, (the direction of the 'wind' in conjuction with the width of the stators...) Wouldnt it be 'timed' to work better one way. (maybee Delta cancelles this out and wye makes it more pronounced...(gaining a bit of efficiency in the favored direction...)
However, NEU's (and most BL I think) are made for planes, so counter-clockwise should be the 'right' direction. (this would be of no help to AAngel's problem, you were going CC anyway right?...)