Out of sync audio for Blu-Ray

Okay first
Win 7 i7, 12 gigs of Ram, the right video cards....
I have 2 sequences the first is an awards show 2:24 mins all edited with lower thirds and credits. Native 1920 x 1080 29.97 .MOV.  This I output from Premiere using H264 BluRay and down scaled to 720. It work fine in ENCORE CS6.
The 2nd sequence is red carpet and green room interviews 1920x1080 29.97 .MOV files all edited with titles and lower thirds. When I output this the same as the 1st sequence, H264 BluRay and down scaled to 720 and then import the files as a time line into ENCORE CS6 the audio is out of sync. In fact it is about 1 sec faster than the video it starts off in sync and drifts.
If I output this sequence at 1920x 1080 no down scaling to 720 then it is in sync but the whole project is then too large to fit on a single layer Blu-ray  disc this is why I have down scaled 720.
I have re-output it 6 different ways and the only way I get sync is at 1080. It makes no sense to me because the 1st sequence down scaled with no sync problems at all.
I even dropped the edited sequence into a new 720 sequence and scaled to frame size then output that and still the audio is out of sync.
Let me say so there is no misunderstanding the audio is in sync on the premiere time line the problem only occurs when output to ether H264 Blu-ray or MPEG2 Blu-ray if I down scale to 720. If output to 1080 no sync problems.
I don't know what to try now but go to a dual layer disc and I really hate to do that and waste 20 gigs of space.
Any ideas?
Thanks
Dennis

If I output this sequence at 1920x 1080 no down scaling to 720 then it is in sync but the whole project is then too large to fit on a single layer Blu-ray  disc this is why I have down scaled 720.
The only two factors which affect file size are bitrate and duration, specs like resolution and frame rate have no bearing.
Try using 1080 with a lower bitrate.

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