Are you able to use the recorded format 25 FPS without problems and forget about 24 FPS?
Why did you not shoot 24 FPS when that is what you wanted. Reshoot seems the simplest approach.
It was shot some time ago for Pal SD and now they want cinema. Reshoot not an option.
I have since rendered out clean 24p files and that seems to have solved issues but as I mentioned I was hopeful that prem would handle originals.
Anyway I will continue with edit now and see if any more issues arise.
Would you have any idea why these problems exist?
Did you try without reinterpreting the clips to 24p? You really just want to conform this, not retime it, I would imagine. In other words, just leave the 25p clips as 25p and edit them in a 24p sequence. It could be the combination of the intepretation and the speed changes (which seem to be the root of many issues in Premiere) that are freaking out.
The originals are interlaced 25fps so to get the best possible results you need to interpret as 24fps so prem (or AE) looks at both fields then pull it into a 24p sequence. The results are very clean.
I think you are right about the combination of the intepretation and the speed changes as my new files seem to be working.
So I guess the rule of thumb is to not interpret from the original file if the edit is complex i.e. ramps/blends/dissolves etc.