I'm using Calbre to transfer my books to my iPad 2 in iBooks and for some reason, a few of my books are showing ? symbols on almost all the pages. I've tried these books in my wife's Kindle with no problem but in iBooks or Stanza, they show up.
These are not DRM books and some are even free domain. This is not on every book but a large number of them.
Any idea why this is happening and what can be done about it?

OK, I think I fixed it but I used Calibre to export the book to another format (from epub to mobi) and used Calibre's plugin option to use a different code when converting. Not that I understand what I did, but I followed some instructions in Calibre's forum.

It's a formatting issue. Usually happens when the book is converted from .RTF, .DOC, or .TXT files to ePub. The fix you mentioned works but I prefer to use .LIT instead of .MOBI. I think it leaves a cleaner conversion.