Heyyo,
Hmm, you might be having a incompatibility prob. Cause before, I remember lots of people got angry that cs_wallmart waypoints would never load n' such. I eventually made my own for that map, and it loaded properly each time afterwards.
I bet tha's the same prob you're getting. Try typing this into the console:
waypoint load
if it says that it couldn't find the waypoint file for the map (it's the map's EXACT name, with the extension .pwf so for example, de_dust2 waypoints would read de_dust2.pwf)
If it says something else, you might as well redo the waypoints.