Whatever the actual reason, my wife re-bought the DVD set of the Lord of the Rings trilogy after switching to the Blu Ray version, citing basically the same reason, and that was just DVD-resolution to 1080p. And she still goes to see them in the theater every so often when they show and thinks they look fine there. Go figure. Maybe some companies are messing with color grading and such in higher res versions, or otherwise applying some sort of filters? Like how The Matrix was made much greener after the first theatrical and first DVD release.
Googling around, it looks like only the extended-edition fellowship blu ray had some fairly severe color issues (much greener than every other release). That might have been part of what she picked up on.
