Those are just the normal black borders that the paper cards have. If you go look at a physical card right now you will see that the proportions are the same too, and just like a physical card has rounded corners so does the card image have those little white backgrounds on each corner. It's just that some image sources probably scan them fully, with the borders, while others crop them out.
Basically, it's just how each source scanned the cards. I suppose you could just delete the zip files for the sets that have those and try re-downloading them from a different source for consistency sake with the other scans, if you want.
Edit: just went and had a look at the scans for each of the three sources XMage uses. It seems the ones with the borders you don't want are from wizards.com, so if it really bothers you try deleting those sets from your images and downloading them again from another source. Here's a comparison of the three sites' scans for the same
Swamp from Avacyn Restored as an example:
magiccards.infomythicspoiler.comwizards.com