Exactly, in my experience serious problems with the Reader Library are usually being caused by a corrupted database. As the Library isn't a particularly well made piece of software it is no great surprise that you aren't being asked if you want to deinstall the database as well when you deinstall the software.
The disadvantage of deinstalling the database is obviously that you have to reload all of your books. For that reason I have started to copy and save the database into a separate folder every couple of days. When things go wrong just replace the current database with the last working one and you only have to reload the books that you have loaded in the meantime (perhaps one of those created the problem).