Adobe Media Encoder Quality Issues  for 4:3 FLV Files

I am working in a 480x360 window for a FLV file. Whether I export a 60 minute presentation or a 10 second pre-roll FLV file, the rendered file quality is distorted and poor. I have done the same work in CS3, but as I changed computers, the CS4 was installed.
With the video presentation, orginally capturing the video is set as .9 Pixel Aspect Ration, but interpreting the footage to 1.0 is also an issue.
The quality of video that is being produced is much worse then CS3 and unuseable in most cases.
Frame Dimensions: 480x360
Frame Rate: Same as source. (29.97)
Endoding: CBR
Passes: 2
Bitrate: 500
Audio: Mono / 48

A couple things:
1) VP6 and H.264 are codecs that operate in "mod16". What that means is that they begin by dividing a video image into 16x16 blocks, followed by 8x8, 8x4, and 4x4 blocks. This makes for a more efficient encode. Your 240 dimension is fine (240 / 16 = 15), but the 515 dimension could be slightly problematic (515 / 16 = 32.1875). The codec will stretch or compress the image to fit into that dimension, and so can result in a lower quality encode. If you can, try encoding at 512x240, by cropping a couple pixels in the horizontal dimension. May not make a big difference, but it's good practice with these codecs.
2) To me, your original encode looks like the product of Adobe's less-that-capable deinterlacing scheme. You're dealing with progressive assets and a progressive target. I'd submit that the reason your 1280x720 encode looks better is that you're using a progressive preset, with no deinterlacing necessary when exporting. One thing you could check is the field order of your original sequence setup--if it's interlaced, I'd say you have your answer. If it's progressive--well, then I'm wrong :) However, you didn't explicitly say this in your original post, but it's worth a look.
If it is interlaced, I don't think you can change that after the sequence is started, so just create a new sequence with the proper progressive settings, and copy and paste the original sequence contents into that one. Now, when you export, there will be no need for deinterlacing.
Anyway, that's my guess...

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