Hmmm....found this comment on the B&N eBook FAQ:
Quote:
* Version 2.5+ is installed separately from previous PC versions at this time. You can still use your previous version to see your old annotations. Just use your Start Menu to open version 2.1 Programs - Desktop Reader - Barnes & Noble - Version 2.1.
* New annotations in version 2.5 will sync going forward with 2.5. We encourage you to begin using 2.5.
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Surprising - it actually installs a separate incidence of B&N software...wonder if that is because of the switch over from PDB to ePub...?