I have had a very similar problem. I had converted some books using calibre from RTF to epub. They worked fine on my SONY reader, but when I moved them to my iPad in Stanza, it would view the first page of text, but then every other page was just blank. If you reduced the font of the first page, more and more text appeared. It was like all of the books text was on the first page.
Same file in iBooks worked perfectly. very strange.
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