Thanks for the reply.
No I haven’t experienced this with other formats, but I mainly work in that format. My first thought was GOP aswell but I can’t see why only the export quicktime conversion tool would do this and not compressor.
It’s done it a few times on 30 sec clips and some longer clips. One occasion it added a few frames just before a transition (fade to black using opacity handles)
Any suggestions before I boycott this tool and just use good ole compressor.