Stewart, I had this problem with Firefox after a recent update.
When I clicked on the bookmark icon I had a load of code pop up on the left, but when I opened them from the top list (
File, Edit,
View,
History
Bookmarks,
Tools,
Help) they were still there.
I ended up doing a re install on Firefox and they've worked great since then.
Its not exactly your problem (I don't think), but thats what worked for me.