Hi there,
To be sure, you work in a PAL region, correct? If somewhere in the flow you move between PAL and NTSC, that might create some peculiar field/frame issues. Does the 50′ have an option to go between the two, or are PAL/NTSC issues moot?
If that’s all aligned, where does the stutter first present itself? Do the prores files look as they should, and once Encore transcodes the files it then starts presenting the stutter?
Trying to see where the stutter begins would help diagnose what stop in the workflow is introducing the issue.
50i 1080 is the final result, correct? Have you thought of stepping down the transcoding (within Encore) to 25p 1080? If the 50i is essential to the workflow, I understand, but to test the 50i against something else might help to see if there is something unique about the 50i 1080 transcode (within Encore) that is the issue.
I hope these suggestions help. I only work in NTSC and only once have I had to pull something PAL.
Best luck,
Paul O’Brien