Aspect ratio problems in exporting HD movie

Hi
I have a movie shot in 1920x1080p HD from a DSLR. It's two and a half minutes long. There's some titles, a few photoshop layers, a flash file and some simple voiceover audio. Nothing too fancy all in all.
All I need to do is convert it in the same ratio so that it can play in Quick Time, but everytime I put it through the AME, it comes back slightly squished (not 4:3, but definitely not 16:9).
I've tried QT, H.264, Mpeg2, default presets, custom presets, everything. In the output box it displays my video exactly how I'd like it, but the finished product comes out differently.
The only success I've had is exporting as an MPEG4 file, and the aspect ratio comes out good, but the video itself is choppy, which none of the others are.
File sizes have ranged from 230mb to 2.3gb, so eventually I'd like to keep this down, but for now I'll be happy with anything!
Thanks for any help...

Thank you so much. Works a treat. That sorts me out for most of what I have to do.
If I can bother you with another question...
I need to eventually put this video into a powerpont presentation created in mac. With a small .mov file that's fine to play on other macs. But I will run into problems when I need that powerpoint presentation to run on a PC. I think I need an MPEG file version to run on a PC.
If that's correct, how do I create a non-jumpy mpeg file that's small enough to go into powerpoint. Can I do that on  AME or is it simpler to convert my .mov file in QuickTime to mpeg?

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