Peter, the Guinness sounds very inviting. Pity I am in Tasmania, Australia.
HDV footage is usually interlaced. JVC cameras are the exception. Canon shoots interlaced and I assume you are 25 fps.Interesting link for the Easy setups. So you have converted all your Canon footage to ProRes 1440×1080. Viewing the files in your edit bin, it should show you your field dominance which should be upper.
Check that your footage in the timeline doesn’t have the shift fields filter and also check that your sequence is set to upper field in the sequence settings. If your edit sequence is ProRes 1920 x 1080 then the ProRes that you captured from the camera will have a value set in the distort tab. Double click a shot into your viewer and click on the motion tab. Under distort it should display 33.3. What this setting does is stretch the 1440 to 1920. If your sequence is 1440 then the distort will be zero on the camera footage and the other files that you made which were 1920 will show a distortion of -33.3 as they are scaled to the sequence. FCP usually does this automatically.
So the fact that you have 1440 and 1920 in the same timeline is usually not an issue because FCP corrects the aspect for you. So to trace the field issue, check the footage is upper, the sequence is upper and the resultant Qt file is upper (stay in the same codec as your sequence). In Compressor your mpeg encode should also be set to upper field. With all those set correctly, you shouldn’t have to deinterlace to fix your problem.
In the 25 frame world it is simple. All video except DV is upper.