Why does firefox have so much trouble retaining bookmarks?
Firefox seems to be very volatile when it comes to bookmarks retention. Loss or corruption of bookmarks is a frequent occurrence often when upgrading to a later version. It has even managed to lose bookmarks recently WITHOUT an upgrade.
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There may be a problem with the file that contains the bookmarks. These artilce may help, Can't add, change or save bookmarks - How to fix and Locked or damaged places.sqlite - MozillaZine Knowledge Base.
Your above posted system details show outdated plugin(s) with known security and stability risks.
- Next Generation Java Plug-in 1.6.0_15 for Mozilla browsers
Update the Java plugin to the latest version.
- http://java.sun.com/javase/downloads/index.jsp (Java Platform: Download JRE)