[Steve Sale] “I shot the film progressive on a Sony HVR-V1U and a Canon HV40, my capture codec was 1050i.”
If the footage was shot as Progressive why did you edit it as interlaces?
But for better quality try sending the sequence from FCP to Compressor directly.
FCP Export (with Compressor) or FCP7 Send (to Compressor)
Use a CBR encoding instead of the VBR method.
Use 7 Mbps for the bitrate and use ac3 for the audio.
Do a test with on 10 minutes of the sequence with the most movement in the video.
The send to/export with takes longer to encode but the CBR method offset the encoding time and it should give you a much better encode from HDV.