Uncompressed 23.976 progressive avi and Encore encoding looks like crap!

Since i'm getting an "internal software error" when I try to burn a DVD from an m2v/wav I export out of After Effects; i've now exported an uncompressed AVI so I can let Encore encode to hopefully fix this problem.
So this 1.54gb AVI is 720x480, 16:9, 23.976fps, PROGRESSIVE.
When I import it into Encore and throw it on the timeline, it looks, and plays beautifully. (i've got a mediavault raid) :-D
I then go into the transcode settings and set it to this:
23.976 [fps], Progressive, Quality 5.0
192 [kbps] 48kHz, Dolby Digital
VBR, 2Pass, Min 1.50, Target 7.00, Max 9.00 [Mbps]
After a quick encode (Dual- Dual Core Xenon), I play back the video, and it has a pulse. It jitters at a regular rate, bump..bump..bump..bump, the text jumps as if its jumping fields. It is overall just horrible, nasty, etc.
So i'm wondering if the MainConcept encoder that Encore is equipped with is just garbage, or i'm doing something wrong. I'm (this close) to going and buying Media Cleaner, or some other aftermarket encodr.
I've got a job to do, and I hate having to trick the software, or change my workflow to get it to work.
Any help would be greatly appreciated!

We'll i've tried both and have not come up with any luck. I've now tried TMPENC, and its pumping out some GREAT looking m2v's. Right now I have to get the settings down, so I dont get an overstream error.
Also, I've noticed that it doesnt mind that its a seperate audio/video stream as it did with my after effects exported mpeg2-dvd files.
I'll keep you posted on my success (lets hope :) )

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