you can only see waypoints when running a listenserver
what kind of message do you get when you start the server ? I mean this HUD text flickering there and showing how many waypoints are used, and evtl. displaying some extra info file.
Are you sure you installed the entire contents of the latest zip archive? It's already configured to load waypoints. If you moved the cstrike/joebot/wpjs/* directories, then you won't be able to load any waypoints at all.
That's not going to work since joebot is expecting it's config files to be in cstrike/joebot/*. It's ok to have the joebot_mm.dll in addons/joebot/dlls if that's where your plugins.ini file is pointing. However, you still need to keep the rest of the files as it's already layed out in the zip archive.