I had the same problem on my iPad you describe, Chookie. Like you I used it with a Windows 7 computer.
It happened intermittently, perhaps more often after an update of iOS or iBook. And then it would fix itself. Have you tried powering your iPad off, and starting again?
Anyway, I traded my iPad2 in for a refurbished mini, and haven't had the problem since.
I second pwalker8's comment about Marvin. I think it's far and away a better ereader than iBooks.
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