H.264 is outputting stretched and low res.

Dear Compressor mavens,
Help me if you can. My issue is this, a month ago I used compressor to take an uncompressed 1280 by 720 HD QuickTime movie output from FCP and make it into a hinted webcast QuickTime at high resolution and it worked great. I used H.264 at 50% of source and it was a dream to watch on the web.
Now a month later I output the same project again, and using the same settings I attempt to make a similar compression. To my abject horror I found that the output was stretched width-wise to an obscene amount.
I checked the 50% of source settings and noticed that the frame size read: 853 by 360. At 100% it reads the proper aspect ration - 1280 by 720. When I choose "custom" settings on frame size and type in the proper aspect ration for 50% (640 by 360) it exports the correct aspect ration.
But to my complete horror there is a noticeable reduction in quality. The image is low res, pixilated around the edges of objects. Clearly not the same beautiful output I originally got from H.264. The really bizarre thing is that the image is the proper aspect ration without that lower res quality at 100% of source on the same setting.
I tried messing with the video settings, by changing the data rate to automatic, then back, then upping the restrictions, and raising the compressor quality to best. Zero change. Still that crappy pixilated image.
I tried switching the Pixel Aspect "Default for Size" to the proper 720 HD setting. To my elation I saw that now the 50% of source reflected the proper 640 by 360. But the quality still looks the same on the output.
I thought perhaps I exported from FCP wrong. But the uncompressed QuickTime is the right aspect ratio and plays great.
Any ideas? I really need to make a high quality hinted compression for the web.
Save me, oh H.264 devotees...

For H.264 on web, I would recommend one of the frame sizes suggested by Robert Reinhardt at http://labs.influxis.com/?p=6
I believe this goes for every codec which makes use of 16 by 16 pixel macroblocks. If you choose a resolution which is not divisible by 16, 8 or 4, you might in addition to lower quality end up with a 1px green border at either the top, bottom, left or right side of your frame.
Have you tried using frame controls in Compressor? Have a look at this post: http://discussions.apple.com/thread.jspa?messageID=7309534&#7309534
There is no need to change the pixel aspect ratio to something other than square. You want square pixels for content displayed on a square pixel display (unless you are making an Apple TV anamorphic file).

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