"Sounds like it can't access its Sqlite database. I've had this before when I've had an instance of Chrome locked up somewhere, and started another process. (That's Chrome for Linux, admittedly, which is still in beta.) One tell tale sign of that - the bookmarks didn't have the proper icons either.
Has this problem persisted across reboots? If you haven't rebooted since you first saw the problem, I suggest you kill Chrome, then bring up task manager and make sure that there aren't any more Chrome processes running. Then restart it and see if it's behaving any better."