On Windows, the positions are saved into the Registry.. and the saving is BUGGED... ironically by the "Save/Restore Toolbars" feature the was added in v8.
It seems each time you get a "scramble" and choose Restore, you get duplicate entries for all toolbars. If you turn off a plugin that has a toolbar, when the plugin is turned back on, Sketchup creates a new Registry entry rather than using the old one.
My toolbar entries in the Registry are up to 566 !! .. Sketchup is taking way too long to parse all this junk at startup.