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Does this happen to just one particular book? Have you tried uploading another and still get this error?
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If you're uploading a PDF file, please ensure it has no encryption. Our system will automatically encrypt your document with military-grade algorithms immediately following upload.
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Adobe's DRM scheme is stringent on the formatting of ePub files. Even documents that go through epub check can get stuck during the encryption phase though that is a sporadic case. We'll dig through our server logs to see if we can produce some actionable items for you to get these up and to run.
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In the meantime, please run the file through the epub check tool at https://code.google.com/p/epubcheck/. Its output could also help identify the problem.