I found this on Sony's forum:
https://forum.sel.sony.com/viewtopic.php?f=54&t=13036
by sonymod_mb » Fri Feb 03, 2012 4:04 pm
Sony has received reports from a number of PRST1 owners that the Reader software has been causing bookmarks and notes to be duplicated with some of their books. Sony engineering is aware of the issue and is currently working on a solution which will be in the next release of the software.
When the update is posted on Sony’s eSupport site we will also announce it here. Thank you for your patience in this matter.