Whamcomics,
What software are you using to edit the images? I use Photoshop, and it has a quirky way of retaining the last compression rating that you used as a default.
When I prepare the cover image, I generally target a slightly higher file size than the interior pages, anywhere from 1.5 to 2 Mb. For interior pages, I try to target 500Kb or less, specially for the 52 and 68-page books, just to keep the final package size small.
My point is, however, I will find that, when editing a book, if I haven't done all the interior pages in succession, my compression settings will not be consistent across files, requiring me to go back and re-compress some.
What Yoc suggested is best: post one of the troublesome books and let somebody take a look. It might be something simple.