Why do my PS video transitions have poor quality on playback?

I've created a slide show using layers and have created a video group. This turns the layers into clips in the timeline.
I've added a cross-fade transition between each clip in the timeline.
Everything plays back nicely in PS.
When I export to mp4 and play it back in Quicktime, no matter what the magnification, the transitions look horrible. Even if I freeze frame on one it's horribly pixelated. I've tried different export options with the same results. Something appears to be happening during rendering the transitions, as if PS doesn't know how to create them.
I export to:
Adobe Media Encoder
H.264
High Quality
1920 x 1080 (same as my file)
Frame Rate 30 fps
Field Order: Preset (Progressive)
Range = All Frames
My stats are:
PS CS6
iMac 27"
10.6.8
800 gigs free space
12 gigs ram 8 free

I don't use Photoshop for video so am having to guess here, but you say H.264 but not what preset you are using. In PremPro there are something like a 100 prest options for H.264  Try something like Vimeo HD 1080p 29.97, but instead of exporting the entire video, drag the markers under the video preview window, to contain just enough to see if it is working.  That will save you a heap of time.     Can you select VBR 2 pass from the Citrate settings in media encoder?  The Vimeo setting of 5Mbs for the target bitrate should easily give you nice transitions, but you can up that if you like, at the expense of file size.

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