Import from EyeTV causes severe jitter

It's a workflow i've used successfully in the past for quite some time. Recently, though, it's been causing some very prevalent audio and video jitter, as well as frame drops/green "content missing" screens.
Source files (EyeTV archive, .mp4 export) all play back with no problems.
Capture is from an HD PVR (Hauppauge) which exports in a native H.264 via .mp4 format (multiple other export formats but all require re-encoding)
I'm able to successfully walk it through iMovie to remove the jitter, but that adds a sizable chunk of unnecessarily wasted time. I'd prefer not to do my editing in iMovie due to it's over-simplification lack of features. I'm by no means an expert, I've probably only scratched the surface of FCP's abilities, but I do do small-time capturing/editing for a videogame comunity.
Neither application has seen a recent update (in the timespan the issue has arised) nor have any of my capture/export settings.

I've known it wasn't the greatest format for editing, basically anywhere, but it was a time and space saver (and up until recently, worked well enough)
Like I said, i'm nothing major. I have no formal training in video capture and/or editing, nor are my products of a professional level.
I've used MPEG Streamclip in the past, It's great, if you have the time. Unfortunately, It's adding another ~45 minutes for every 10 minutes of footage to my workflow, something I can't afford on a daily schedule.
I'll give a transcode another shot directly out of EyeTV, but i'm not expecting any faster results.
I've tried to optimize (both optimize and proxy) the footage on import to FCP. In some instances, it's completely corrupted the copy that FCP works with (dropping frame rate down to 2-5/second, dropping audio/video, significant distortion ETC), and other instances, it's done nothing but waste my time. (I.E. i've never had it do anything beneficial)
Until I find an efficient workaround, I guess i'll have to stick to iMovie.
Thanks for the help anyway, both of you!

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