APR Sequence settings

Hi,
Is there any difference having a sequence:
1. APR LT
Aspect Ratio: Square,
Filed Dominance: UPPER,
and
2. APR LT
Aspect Ratio: Square,
Field Dominance: NONE ?
I had AVCHD files transfered to APR with Toast, put them in the timeline, change sequence settings? YES, and I got number 1, (Square - UPPER). Then I got another video, QT H.264, transferred to APR, put it in the timeline and got number 2,
(Square-NONE). Just curious about the difference, and the final quality. Thanks!

Johnny