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Can you post a segment of this video showing the stuttering to YouTube so we can have a look?
Which Share path are you using to create your output video? Are you using Share/Computer/AVCHD 1920x1080? Where do you ultimately plan to display your video? (On a DVD or BluRay? On YouTube? On an iPod or iPad?) There are unique specs for your video for each of these final destinations.
Also, if you use Share/Computer/MOV to output a standard def MOV and play it in Quicktime, do you see the same stuttering?
My share path was Share/Computer/AVCHD/MP4-H264 1920x1080p
Ultimately the clip probably ends up in youtube / other web video service (and I can use the proper preset then) but here I was looking for the best possible quality to use for viewing on my computer / tv via the WD HD Live box.
The test clip I uploaded to youtube worked just fine there even though it showed the stutter problem as a mp4 file on my computer.
And having further studied the issue, the problematic mp4-file plays just fine if I move it to my SSD drive instead of normal hard drive or if I export the file with slighly lower bitrate... I'm running fairly new computer so this option didn't even occur to me. Especially when the WD Live box exhibited the same problem.
So this was a completely pointless n00b-problem...
Thanks for your answer anyway!