Usually when this happens I just reopen the menu and save it again. Even if I don't make any changes to the menu, this seems to fix the problem. But this last time it didn't. So I copied the menu folder down from my remote host where it did work and that fixed it. I had updated some menu points (as I replaced # with actual files) that weren't on the remote host, so I had to do that again, but that was no big deal.
Maybe now that I have the HTTP on the local tab correct it won't happen. I'm just guessing (and hoping).