You may have a corrupt localstore.rdf file. https://support.mozilla.org/en-US/kb/changes-toolbars-and-window-sizes-are-not-saved

This did not help. Items on the toolbar still disappear, even within the same browsing session - it's not just when I restart Firefox. It happens when I open a new tab, when I switch between tabs, etc.

Your System Details shows;

Installed Plug-ins

Adobe Shockwave for Director Netscape plug-in, version 11.6.6.636 Adobe Shockwave for Director Netscape plug-in, version 11.6.5.635

Having more than one version of a program may cause issues.

Remove 11.6.5.635

Start Firefox in Safe Mode {web link} While you are in safe mode;

Type about:preferences in the address bar and press enter

Select Advanced > General. Look for and turn off Use Hardware Acceleration.

Poke around safe web sites. Are there any problems?

Then restart.

No, none of the above helped. I got rid of the Shockwave plugins completely, shut off hardware acceleration, re-initialized pluginreg.dat... nothing.

Frankly, I think this is a problem with Sync. sync refuses to acknowledge that I have changed the toolbar and puts it back to the way it thinks it should be.

Try to reset the browser.uiCustomization.state pref on the about:config page.

If you keep having problems with preferences, see:S

• http://kb.mozillazine.org/Preferences_not_saved

Nope, that didn't work, and neither did the methods in the article.

However, I have been able to prove that it is not, as I thought before, related to Sync.

Here is the line item from prefs.js that you referenced:

user_pref("browser.uiCustomization.state", "{\"placements\":{\"PanelUI-contents\":[\"edit-controls\",\"zoom-controls\",\"new-window-button\",\"privatebrowsing-button\",\"save-page-button\",\"print-button\",\"history-panelmenu\",\"fullscreen-button\",\"find-button\",\"preferences-button\",\"add-ons-button\",\"developer-button\"],\"addon-bar\":[\"status-bar\",\"addonbar-closebutton\",\"flashgot-fake-tbb\"],\"PersonalToolbar\":[\"personal-bookmarks\"],\"nav-bar\":[\"flashgot-media-tbb\",\"urlbar-container\",\"abp-toolbarbutton\",\"igmail-notifier\",\"downloads-button\",\"search-container\",\"firebug-badged-button\",\"webrtc-status-button\",\"nav-bar-customization-target\",\"nav-bar-overflow-button\",\"PanelUI-button\",\"window-controls\"],\"TabsToolbar\":[\"tabbrowser-tabs\",\"new-tab-button\",\"alltabs-button\"],\"toolbar-menubar\":[\"menubar-items\"]},\"seen\":[\"abp-toolbarbutton\",\"fngmail\"],\"dirtyAreaCache\":[\"addon-bar\",\"PersonalToolbar\",\"nav-bar\",\"TabsToolbar\",\"toolbar-menubar\",\"PanelUI-contents\"],\"newElementCount\":0}");

For reference, on the gmail notifier (sometimes) and flashgot stay on the toolbar. Adblock, Firebug, download, and the search container all disappear regularly.