When I export an mpeg using the Adobe Media Encoder export function (originally from 1440x1080 HDV source, 60i footage) and export as MJPEG B codec .mov file container, I've noticed that if I add any type of levels and contrast adjustments, the video deinterlaces itself while exporting, even when I don't have the 'deinterlace' checkbox clicked.

I've now started to export as Movie... in the export settings and setting everything up that way, but the media encoder was simpler to have ready to go by having defaults set. When using the export as movie it works fine, no issues with it deinterlacing when I didn't want it to.

Anyone have this issue?

It's hard to help you pick the best codec without knowing what you want to ultimately do with it.

If you want an intermediate codec, MJPEGB isn't something I've seen anyone use. Actually, I haven't used any MJPEG codecs for over a decade. QT with the Animation codec is lossless and dead reliable as an intermediate. The files it makes are huge, but it works like a Swiss watch. You can deinterlace or not without issue.