Captivate 5.5: Problems with export SWF to MP4

I recorded a screencast of several moving graphs by using the FMR-mode in Captivate 5.5. The flash file looks pretty good, but I am unhappy with the MP4 that I exported afterwards because it is jerky. Is it usual that there are losses due to the compression or did I just use the wrong settings? Is it possible to export an MP4 file that looks just as good as the SWF? Do you have any recommandations regarding the settings?
I am inserting some features with Final Cut afterwards. To avoid further compression losses, I would appreciate some hints regarding the settings in Compressor. The final file shall be an MP4.
Do you think with the HD screencast function of Captivate 6 or 7, my problems would be solved?
Thanks a lot for your help!

Hey Lilybiri,
thank you for your answer. I tried pretty much everything, default settings like SD / HD widescreen as well as custom settings in all different kinds. I even implemented a 30 frames-extra (http://www.tecwriter.de/wordpress/captivate-5-5-exklusiver-spezialtipp-mp4-output-verbesse rn/), but nothing helped. and i am not sure, if captivate's FMR function is the problem, as the swf is much less jerky.

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