Jittery encoding using the Vimeo 720 preset

I upload 720 versions of projects to Vimeo for clients to approve and the preset has worked beautifully...until the last few weeks. It started right before the upgrade to 2014 CC. The encode would be all jittery upon playback (audio was fine, video was not). It seemed to be fixable by restarting the computer and re-doing it. And it also seemed to get fixed with the upgrade to 2014 CC. But it's crept back into the processing and this time restarting doesn't help. Encoding it to 1080 and uploading that works fine, but as that slows things down considerably in regards to uploading it/having it process on Vimeo's end...and since I also like to do a 720 version of the overall project to give to clients as well (on long 2-hour shows)...it's getting to be a serious problem.
Any ideas what could be causing it? I'm using the new MacPro and haven't installed any new software other than 2014 CC (and as I said, it was happening before that)

I imagine your encode time is the killer plus the export. I can't help you with the export part but the encode time I might be able to.
We've started using the Elgato turbo.264 HD usb-encoder and have been fairly happy with it. The colors get a little washed out and there are some artifacts (more than I'd like) but the time savings is immense. You can also use it from within Compressor.

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