I can't remember off the top of my head, but if the bot derives its configuration folder in relation to where the dll itself is located, it might be possible that it can't find the waypoints..... I.E., you put the dll in hl/dlls/, then the bot might try to find the waypoints in /hl/shrikebot/waypoints. Try putting the dll in the proper place.

BTW, if no waypoints are found on a dedicated server, you will see "Waypoint File [mapname].wpt not found!" in the console. Hope that helps!