At least one page still has an alpha channel. Try to automate removal of that so you can get consistency without having to worry about it.
You're getting minor bleedthrough. Try placing a sheet of black construction on top of the page when you scan. It's easy to do and significantly cuts down on bleedthrough.
I see gutter shadow so I assume you didn't take this apart. I don't know how well black construction paper works with a non-dismantled doujin, but I think it's still worth trying.
Thanks for the feedback. Is it best to remove alpha channels before or after leveling the image?
I'll try to see if using black construction paper can help reduce the bleedthrough in scanning pages. I've been struggling to minimize this sort of thing for a while now, and I don't see why it wouldn't work with non-dismantled pages (I always put weight/pressure on the scanner cover with a folded piece of cloth placed on top of the book to minimize the "tenting" of the book).
@grgspunk >Is it best to remove alpha channels before or after leveling the image?
Probably as the very last thing you do with the file before uploading them. It's being added when you rotate the page (that's what GIMP does, don't know about photoshop). After the rotate it's not going to do anything except take up space. But there's no point in removing it immediately, in case something else adds it back later (e.g. adding a new layer to erase some dust/scratches).
Photoshop might be able to automate this, but I haven't a clue how. Manual option in GIMP: Layer -> Transparency -> Remove Alpha Channel
Imagemagick can do it as well. In a command prompt window: for %f in (*.png) do convert "%f" -alpha off "noalpha_%f"
In a batch file: for %%f in (*.png) do convert "%%f" -alpha off "noalpha_%%f"
...that creates a copy of each file named noalpha_ whatever, so there's probably a better way to do it.
(Modern imagemagick uses "imagemagick convert" rather than just "convert", I think. I haven't gotten around to upgrading)