Out of curiousity, what OCR program were you using?
I've been meaning to try out various OCR options for linux (Tessaract, Cuneiform, Ocropus, etc.), but just haven't found time for it. If I get around to it, I'd be happy to swap notes.
A lot of people around here rave about ABBYY finereader (Windows) for OCR, and I'd imagine it can handle both these desiderata, though as an open source enthusiast, I always like to see what other options are available before moving to commercial tools.
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