Media Encoder  output size vs. input size

I'm having trouble preserving the qualities of the source in the output
The source, imported into  a .Prproj is:
Video: MPEG4 Video (H264) 1920x1080 23.975fps [VideoHandler - MPEG4 Video (H264) (eng)]
Audio: AAC 44100Hz stereo 116kbps [SoundHandler - MPEG-4 Audio (eng)]
and about 25mins in runtime with an on-the-disk size of 1,269,xxx KB
the output result after saving .Prproj and importing that into Media Encoder CS5.5 then encoding:
Video: MPEG4 Video (H264) 1920x1080 23.998fps [Mainconcept MP4 Video Media Handler - MPEG4 Video (H264) (eng)]
Audio: AAC 48000Hz stereo 157kbps [Mainconcept MP4 Sound Media Handler - MPEG-4 Audio (eng)]
and about 8mins in runtime with an on-the-disk size of   1,322,xxx KB
the specs are close to identical, and from my mind, not different enough to cause a sequence roughly 1/3 of the original to end up being physically larger than the source.
All the other formats and presets don't (seem to) allow for anything close to the original specs.  I found the dropdown for the audio to be set to 44100. I realize that's trivial to the data load <smirk>
I'm pretty ignorant to the effects other options can have -- and I presume that the options pre-selected by ME are grabbed from the source.
Am I wrong or is there anything I'm missing?  another codec would help (the Mainconcept is a hog?)
If so can anyone direct me to one and the directions for having ME make it available?
thanks for any help you can offer!

The AVI file plays with the correct dimensions in Windows Media Player, and the Quicktime version also has the correct dimensions. I don't have Premiere Pro, and I'm using the version of AME that came with the Design Premium CS4 package.

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