Quicktime conversion

Feel a little silly raising this here, QT conversions are something I thought I knew enough about not to need advice, indeed I've often given it, but I've had some quite strange results exporting my latest project and wondered if any one had any comments on my observations.
My projects are AIC 1440 x 1080, my main video source is a sony SR8 (AVCHD 1440 x 1080i) but I invariably add a number of stills, titles and sometimes even video from other sources. My output is aimed at my tv and web gallery for general viewing over the internet, but I maintain my projects intact for someday when I may want a higher quality delivery format.
As such I have generally found the easiest method with reasonable results has been to export from FCE as a quicktime movie and import that into imovie 08 which will handle all the export formats and resolutions I require as well as undertake the uploads to my web gallery. I have exported numerous projects in this way and been reasonably happy with them in the past.
However I was dissatisfied with my latest 960 x 540 h264 export from imovie in that large areas of similar colouring were not satisfactory (sky, walls, water etc) and there was also too much motion judder introduced. (I've come to expect a little motion judder with panned shots and h264, but this was above my expected level)
Resulting from my dissatisfaction I tried a few different export techniques from both FCE and imovie, but bare in mind I've tested various export options on many occasions before and have not seen the results I'm about to describe.
I'm not as worried about my exports for my web gallery as I am about my export for the tv, so the settings I experimented with were made with this in mind. I tried exporting as a MOV with h264 encoding, as an MPEG4 with h264 encoding and exporting using the tv preset and with the exception of the preset I tried both 720p and 540p (I'm working with 25 fps). I was surprised that in every instance I found that imovie provided a better output and indeed the best output was provided by the simple export to movie (540p) from imovie (which I don't believe has a comparable setting in FCE.
To add to what I thought was already very strange, I noticed that settings appeared to be getting stuck, I'm not so sure I can explain this very well but I'll try.
During one test, which I think was an export to MOV, I checked the de-interlace source video and ended up with de-interlacing artefacts in the export that had not been there when I exported using the same settings but without checking the de-interlace option. I didn't actually think there was very much odd about this until I unchecked the de-interlace option and exported again and the artefacts remained.
To summarise:
Export 1 - de-interlace unchecked, no artefacts in export.
Export 2 - de-interlace checked (other settings = the same), artefacts noticeable.
Export 3 - de-interlace unchecked (other settings = the same), artefacts noticeable.
I also noticed that if I made an export (call it Export A) and noted the settings and then made a few changes for subsequent exports that if I returned my settings to those I had used for export A and exported again, that the new export was significantly different to the original export A.
I don't believe these things should be happening, anyone noticed anything similar or know of anything that might be causing this.

I've tried with to source formats; the first was beta sp transferred to mini dv which I captured from my deck. the other was 24p mini dv captured from my deck.
settings: VIDEO: vid. comp= h.264; qual = High; key frame = 24; frame reordering = yes; encoding mode = multipass AUDIO: format = uncompressed; sample rate = 44.1; sample size = 16; channel = 2
I need to convert to a normal quicktime file and use in a premiere project. I've done it several times before but now something's weird.

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