In VP, set project property to top/bottom full and render, use a larger bit rate of 48mbps (24 mbps for each stream for the 3DA1). Then import into PD, right click and change 3D type to top/bottom. Then you have full 3D from AG-3DA1, that's the way I do it. I also do this for 3D menus in PD. Yes, you can keep the clips shorter in VP. For me it was over 12 minutes with that audio problem. I forgot to mention, I did have a problem with PD before I upgraded and that was with DTS audio for Blu ray, it would cause problems, there was an update which fixed a DTS bug, but I think I still had issues because of the larger bit rate. AC3 didn't have this problem. After I upgraded the problem went away.
Oh, and you'll probably want to keep your interlaced footage separate from this render so you can get a good 30 to 24 frame rate change, if you're using footage from both cameras.
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