Just happened with me; Ubuntu 8.10 + Firefox 3.08. BTW, I did previously
try to run "sudo firefox". Normally this would start another Firefox,
3.1b3, which is installed for root user, but that time 3.08 started.
When I later tried to run Firefox as normal user, all the bookmarks were
gone and FF reported it as unable to restore them from backup. Moreover,
when I open a web page by clicking a link, the address bar does't change
(actually it remains empty). The icon next to the tab title shows that
the web page is still loading, although in fact it's loaded.

Running "firefox" from terminal gives the following output:

Torbutton logger online
[04-24 17:21:29] Torbutton NOTE: Skipping no location: 
chrome://browser/content/browser.xul


I've installed Torbutton, as you see.  But Error Console gives the following 
error, repeated for several times:

Error: [Exception... "Component returned failure code: 0x80570016 
(NS_ERROR_XPC_GS_RETURNED_FAILURE) [nsIJSCID.getService]"  nsresult: 
"0x80570016 (NS_ERROR_XPC_GS_RETURNED_FAILURE)"  location: "JS frame :: 
file:///home/admins/.mozilla/firefox/w544d3yb.default/extensions/%7Be0204bd5-9d31-402b-a99d-a6aa8ffebdca%7D/components/ignore-history.js
 :: anonymous :: line 67"  data: no]
Source File: 
file:///home/admins/.mozilla/firefox/w544d3yb.default/extensions/%7Be0204bd5-9d31-402b-a99d-a6aa8ffebdca%7D/components/ignore-history.js
Line: 67

The mentioned JS file in attachment.  Later I'm going to try the
mentioned solutions..

** Attachment added: "ignore-history.js"
   http://launchpadlibrarian.net/25935457/ignore-history.js

-- 
Firefox 3 bookmarks lost after unclean shutdown
https://bugs.launchpad.net/bugs/241609
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