I had a similar problem. It just completely froze while I was reading, the screen did not respond to anything just the home buttons was working. I had to close it and restart it to have it working again and lost 3/4 of my books. Calibre didn't like it, because there was database problems. So I had to do a factory reset and this time loaded my books manually. I thought it was because the calibre driver is still experimental it messed something up. But reading your post seems like something very similar. I do hope that it will not happen again, because resetting it and reloading everything is a pain.
ePubFixer - http://code.google.com/p/epubfixer/
Edit your TOC, by Adding, Renaming, Shifting Chapter, Change chapters order or nest chapter into Part or Book easily by Drag and Drop. Split files by Chapters & Auto Detect phrase for your chapter heading. Also edit the reading order, fix margins & Edit your file with Sigil and restoring your previous TOC that was lost. Edit your cover without reconverting the file, Create an Inline TOC