No presets for 60fps in adobe encoder

I'm new to this software but in media encoder 6 I dont see a preset to encode my 60fps source .mts video in?  I also don't see a way to make an mpeg4, only mpeg2.  Other than the youtube version that is 29.97 fps.
Also I had made a video in adobe premiere 6 using about 3.5 minutes of source footage from my canon vixia hfm31 camera.  shot in .mts format 60fps.  My original mts files play smoothly and I encoded a final video with a song that played smooth.
However I wanted to change some things so i went and reshot some footage also in 60fps, and started mixing them in with the original footage and now whenever i try and encode a lot of the shots are a little choppy.  Like when the camera pans/tilts or zooms out its not totally smooth its a little laggy/choppy.  its subtle but it bugs the hell of out of me.  I've tried using different presets and using the maximum render quality and frame blending to no avail.
What determines how smooth a video encodes?  Is there something I can do to remedy this?

That thread was marked as answered and it seems to have fixed the issue for certain types of files. I am opening a new thread just hoping to get a response from Adobe on timing. I assume they are going to enable playback in bridge for m2ts files at some point. I am just wondering how long it's going to be.

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