Thanks Craig. Sorry I missed this reply when you posted it. Very helpful.
I will definitely investigate Telestream.
I can see my comment was indeed “fuzzy” so apologies for that. I still find the language of interlacing/deinterlacing confusing! What I meant was that the original footage/fcp viewer showed none of the jagged lines but after attempting to make it to H264 these horrible jagged lines started appearing during motion sequences. The original footage was shot on a Z1 so it would be interlaced I assume, but in the “good” way (that is without the jagged lines). I suppose I’m still confused as to why these lines appear when changing codec…
The advanced edge detection and motion compensation options in compressor brought in estimates of 16 hours plus for the compression which wasn’t really an option on the deadline I was on.
For what it’s worth: I eventually solved the issue by compressing in MPEG streamclip. I don’t understand why but it seemed to work.