Why does my frame size change when transcoding?

My movie files are 720x534, NTSC D1 Square Pixel. When Encore transcodes them they become 720x480 which clips off the left and right sides of the movies. Is there any way to get around this, either by rendering the movie files differently in AE or controlling the transcode in Encore?

I hope Todd Kopriva drops by and adds his two cents, since an AE expert may shed some further light.
From Rick Gerard's Understanding the use of square vs non-square pixels in AE:
Standard Image and Composition settings for DV projects:
The proper standard size for a square pixel composition that is going to be FIT into NTSC DV at 720 X 480 is 720 X 534
The sentence after that one is:
For Square pixel artwork that is going to be used directly in an NTSC DV 720 X 480 comp the proper size is 648 X 480.
I don't understand the full implications, but I think you do not want to fit your composition "into" NTSC DV, you want to use it directly.
I'll also note that the Gerard piece appears to be from 2001, so, while it may still work fine, I wonder if the PAR changes as of CS4 complicate using it. I like the Meyers piece on this now.
Here is Todd's blog that has several relevant links, including one to the Meyers piece.
http://blogs.adobe.com/toddkopriva/2009/07/pixel-aspect-ratios-in-after-e.html

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LivelyJamesS wrote:
I exported a short video of mine from Final Cut Express and the size of the file came out to 7.3 GB. When I put it into an iDVD project, it says that the file is only 800 MB.
Guessing here but it looks like you edited/exported an SD/DV sequence of about 30 min in FCE. DVD needs to be MPEG-2 so iDVD compresses the original file down to the size that you report.
LivelyJamesS wrote:
I guess my first question is: why is iDVD changing the size of the file? I want the quality to be the best it can be, so keeping it at 7.3 GB as opposed to 800 MB is rather important.
The quality will be what the MPEG-2 compression and the software allow for. MPEG-2 is DVD standard .... there's no way around that.
LivelyJamesS wrote:
Secondly, why did the dual layer discs come out unusable? I've burned single layer discs before and they haven't been an issue. Also, I know for a fact that the drive can burn dual layer discs, so that isn't the issue.
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Why does my frame size change when transcoding?

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