1) "Yes I did, it's the actual size of my source that's 1440. Sorry."
I'm confused: after you captured 1440x1080 -- what was the frame-size of the AIC file?
It used to be 1440 x1080 (1920 x 1080), now it's 1440 x 1080 (1888 x 1062)
2) "However, I'm now able to export to 1080i (1440) again without such issues."
You originally said you couldn't export at 1080i without it looking bad. Only 540p looked OK. Now you say that you can export 1080i60 ..."
1080i/50
Exactly, what setting are you now using?
AIC/HDV 1080i-HD 1440x1080 (clean)
Is the 1080i60 export free of crap?
(50) Yes.
If yes, why is it working now but it didn't before?
Honestly don't know, I'm guessin I made that many exports at different settings through im09, it messed up. I did get to the stage where the same settings didn't give the same results each time. After you pointed out that  may have changed their default aperture settings, I tried exporting to AIC/other- HD 1920 x 1080 (classic) (since there is no 1440 classic setting), as you suggested and bingo! so I drew the conclusion that only that setting would work.
My previous exports to 1080i (1440) had produced interlaced video with combing as well. I say combing but it wasn't, if I checked single field or de-interlace in QT props I got wavy edges where they should be vertical lines, sort of like 5 or 6 consecutive lines had jumped a millimetre to the left and the next 5 or 6 had jumped a millimetre to the left.
So I may have misled you on that one.
What are you using (QT Pro or JES) to externally de-interlace the 1080i60?
" ... without an issue in QT."
Is your sentence backward? Did you mean "In QT Pro I externally de-interlace 1080i to 720p?
If so, exactly what are you doing in QT Pro to de-interlace?
I don't mean to be picky about language, but if you now can get clean 1080i60 and/or 720p30 -- then you have overcome the major problems with iM09!
No problem about the language, I have difficulties in putting thoughts into words, my mind races ahead so I forget exactly what I'm typing at the time, I try to re-read as much as I can, but long posts are hard work. I don't have any issues about being told about it, in fact I'd rather people do, when it's hard work typing, it's no fun waffling on if someone doesn't understand me, better I find out sooner than later and waste my time.
If I take my 1080i (1440) or any 1080i for that matter from my im09 export and deinterlace and convert it to 720p in JES (either single field or field blended deinterlace) , then yes it is clean. I can also deinterlace in JES and then convert to 720p in QT (I know no-one would do this, it's just for information) and it's clean.
So with a little work I have 720p from im09, albeit with a bit of help from JES.
The bit that I don't understand is where the problem lies. It would seem in one way that QT is the problem in that it simply makes a real hash of deinterlacing, this seems true whether going through the QT interface or the im09 interface. If so then the problem must have been in QT prior to installing im09 and I simply didn't notice it.
This may also be true, I posted some of my source video on my idisk and someone who is still running im08 and QT 7.5.x ran it through both applications for me. They reported that through QT the 720p output was awful whereas the output from im08 was fine.
So perhaps the problem may lie with QT and that something in im08 corrected it, whereas what ever that was has been omitted from im09, sounds absurd I know. Of course 1080i source exported from FCE at 720p is just fine using QT conversion.
To add confusion if I use mpegstreamclip on my 1080i (1440) video to output a 720 QT movie/mp4, if I select deinterlace all is well (as I would expect), if I don't select deinterlace the export is not interlaced but our problem returns. I would have expected the later to be interlaced (but even if it wasn't it shouldn't be messed up).
I hope this helps rather than confuses things more.