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First, what software are you using to put your books on to your reader? If you are using Sony's software, I can't help you much since I have never bothered with that unfriendly and limited software - I would heavily suggest the free software called Calibre for managing your ebook library and reader. If you are using Calibre and if you don't find your answer here, you should post your question in the Calibre forum for better help.
Anyways, here is an attempt at solving your issue:
1. Take a look at your reader when it is plugged into your computer via your finder/explorer (not the reader/calibre software) and go to the usb drives associated with your reader. There will be at least 2 drives - one for your reader's book/pic/music library and one that is called setting that hold's the sony reader software installation. If you have a memory card, there will be a 3rd partition that represents the card. Look at the partition/drive(s) that hold your books and look to see if there are duplicate books. If so, feel free to delete all duplications and disconnect your reader and let it rebuild its metadata file automatically. If this solves your problem, then the problem was with how the sony library or calibre puts your books onto the reader.
2. If there are no duplicates on those partitions, then the metadata database on the reader is corrupt. If so, you can simply delete the metadata xml file on the reader and have the reader rebuild the file and hopefully that will fix your issue. An alternate way is to simply reformat the reader done in the reader's Settings > Initialization > Format Memory command.
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