i've noticed this on a number of projects i was just consolidating the past few days. I had been using premiere pro 23.1, updated 23.6.2 (issue persisted) then also tried the most recent version of premiere build 24.1. The issue again persists there.
This is occurring with any sequence who's framerate is not a whole number, so 25, 30, 24 fps sequences with matching framerate clips are all render & replacing precisely. However if i have say a 3840x2160 23.98 clip in a matching sequence and do a render & replace, the resulting clips are slipped two frames to the right. I identified this first with a sequence that was made of a flattened edit which I had used Scene Edit Detection to make cuts. The auto detection is dead on. however if i do a render & replace to H.264 the first two frames of every clip is the last two frames of the previous clips.. it's immediately apparent when working with a flattened edit that had cuts created via edit detection.
This is reproducible with either sequence, clip or preset source within the Render and Replace dialog. I've tried quicktime and custom h.264 presets with fixed (matching of course) framerates, issue is consistent.
I did some searching and haven't found any reports of this.
I'm on a mid 2015 mpb running OS 12.6.5
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