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It doesn't help you with your problem, but I avoid the issue by how I scan in. I use the free version of Aabbe OCR software (not 100% sure of that name, as I'm not on my home machine at the moment). It uses the scanner's native scanning app to scan in the pages. I scan the first page, then start scanning a second page. In the time it takes the scanner to scan the second page, I can mark (outline) the text on the first page that I want converted (which excludes the page number and the header/footer), and have the OCR software 'read' it. Then flip the page, start the third page scanning, and mark the desired text on the 2nd page and read it. At the end, you have the entire text OCR'd minus the headers/footers/page#'s and in basically the same amount of time as it takes to scan WITH those items included.
When scanning a paperback book, two facing pages are scanned at once. I save the OCR'd text as an RTF and load it into Open Office. The facing pages come up as two columns of text on each page. It's then a pretty easy process to convert everything to one column and get rid of the extraneous page breaks, and you're now ready to proofread and convert to whatever format you like. I like saving it at that point to HTML as a "base format" from which you can then convert to whatever you like, but your mileage will undoubtedly vary...
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