I use FCP very sparingly and am by no means an editor. Please keep this in mind.
I shot a series in 23.98 on a sony f3. It was broadcast in 1080p 29.9. The editor, using an avid, rendered 1080 29.9 QuickTimes of each show and gave me a copy. When I play it on my computer (mac book pro running OS 10.6.8) every 2 out of 5 frames (or sometimes every 1 out of every 4 frames) have horizontal lines running through any part of the image that has movement. I understand that the lines are because it is showing me two different fields at once. My goal is to have copies of all these episodes withOUT the shitty horizontal lines. What I think I need to do is re-render the files as Apple Pro Res 422 (HQ) 1080p 24 QuickTimes. I did some tests. Some were successful some were not. I’m using FCP 6.0.6. I created 10 sec cut of the show. I went to export and selected QuickTimes. Then I selected Apple Pro Res 422 (HQ) 1920 x 1080p 48khz and the test was perfect. No crappy horizontal lines. Then I rendered the whole show. Which is 22 minutes. And the horizontal lines were back. Wierdly, I was able to export the whole show without the horizontal lines in 720. But I need it 1080.
Removing pulldown is tricky. You can't just render it out at 24p and all will be OK. You need to do tests to figure out what pulldown is used...what pattern, and how to remove that. Cinema Tools removes pulldown. But you will have to test on small clips to make sure it is done right.
your tests at 720p worked as 720p is a progressive format, so everything was deinterlaced. 1080i is interlaced mainly, but can be progressive.
You can also remove pulldown, or convert it, with compressor. Again, you will have to test on small sections to see what works best.