I wasn't online a long time, but I believe,
JoeBot is not yet compatible with 1.6.
So how it should create some WP's !?!
Just wait ... and soon the offline version of CS 1.6 is available.
Then the developer of it is able to update his bot.
It only a question of time !!!
It's not the waypoint files. The version you have has a bug where the bots get the wrong max speed at the beginning of a round. Compile the latest source to fix the bug.
Then only map that requires a cs1.6 specific waypoint file that I've found so far is de_aztec.
The currently best way is to grab the sources from the CVS at sourceforge.net and compile it by yourself.
Or you can try the version I compiled for my server (debian 3.0/testing). Unzip to the $hlserver/joebot folder (you also need joebot-1.6.1-linux for the other files) and add the line