The update fixing this issue (among other improvements) is now live in the App Store:
http://itunes.apple.com/app/id301259483?mt=8
Quote:
What's New in Version 5.4.1
★ Improved typography and styling
★ Enjoy crisp text and images on the new iPad's Retina display
★ Share and view public notes that are tied to specific passages
★ Get notified when someone replies to your public note and directly access the thread with a single tap
★ Re-designed homepage to include your recent reads and access to popular free books & free classics
★ Customer-requested bug fix for books disappearing when using an unreliable network
★ Significant performance improvements and bug fixes
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