So, if you’re not using Compressor, you must be using Quicktime to do the encoding, and neither Quicktime nor Compressor will make a blu-ray compatible H.264 file. So, what’s your secret, Joseph?
It does sound like a field order issue, however, I recall that the XL2 does not have 16×9 chips, which means that it does a pseudo 16×9 by blowing-up the 4:3 image. This would result in a softer image, and possibly some jaggies.
I just did the same thing and observed the Preferences folder as I opened and closed various Quicktime movies in QT7 and QT10. There is one preferences file for each version of the player. Every time I open a movie in one of the players, the preference file is updated, but an additional one is not added.
If you’re using EpsonScan software, you need to be in Professional Mode. Then, you can change Target Size from inches to pixels. Enter the dimensions, and then save that setting. All your scans will be locked-in to that setting. Understand that you will be cropping your photos to a 16:9 aspect ratio.