The scanner in the Phaser 3300 will always scan the entire length of the platen and, by default our software will crop 5mm from the edge but no more than that. However, the image capture program on the Mac will auto crop white space if you tell it to detect different sizes, this can be up to an inch. I think that this is what you are seeing - so try to turn that feature off in your Mac and let me know if that resolves the issue.
So if I use the document feeder and just tell it to scan like mad, everything is perfectly OK and I can scan. Many of my documents, though, cannot be fed through the feeder (receipts, etc).
When I use it as a flatbed scanner, the top inch or so of every page is lost. If it's a landscape orientation, the right (or whatever side is facing the "top" of the bed) side is lost to the same extent. This is even more of a problem if I'm trying to scan multiple distinct items as different documents at the same time, as there's no real method for deciding when it's going to queue up too low or not.
It previews perfectly, so I'm guessing that there's a driver issue. So, is this a known issue, or is there a magic button that I'm missing that the manual doesn't mention either?