Welcome to the forum.
This is but a wild guess on my part, but unless I mixed things up, it's the QT Reference, that is taking the longer to process. That guess is that PrPro is needing to "fill in the blanks," on the Reference File. Why one, nearly identical file would show MPEG, and the other QT Reference, is a mystery to me.
Also, I'm a PC-guy, but do work with a lot of MOV files from outside contractors (mainly 3D animators), but I specify MOV Animation, and those work just fine.
I hope that others will have something useful for you, beyond my guesses.