You can install 32bit application on a Windows 64, kind of just works. Don't hesitate to pick 32 bit version, even if you have a 64 bit OS.
Have you contacted bookeen about the vista issue ? The gen 3 is just a mass storage device, should work with any OS.
(just as a side note, 32 bits OS will be able to use only 3G of ram, so if the PC you plan to buy have more ram than that, go 64bit.)
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