Kiwi mentioned once that the way he gets it to work on Windows is writing a batch file with predetermined generic filenames, renaming the scanned images to match the names in the batch file using a bulk renamer, then renaming them back when they've finished processing. It's a little slow, but you can do something else while it's processing, and in the end it's a lot faster than doing each page manually.
Besides, weren't you the one who said he was going through issues of EGM we already have uploaded and straightening them out? This deskew utility would help a LOT, I imagine.
http://galfar.vevb.net/wp/tag/deskew/