It is not possible to run on waypoints. If it were then it would work. I cannot get it to work. However, you can run to targets. You were only asking about waypoints. Here is the code to set and run to a target.
;Artificial Intelligence Script
;Header
desc = run to target
;Triggers
:state=0:etimerstart,state=1
:state=1,etimergreater=1000:settarget,settargetname=target1,state=2
:state=2:animate=5,movetotarget,state=3
;End of Script
The etimer is used in this test so that the npc hesitates as the game starts so you can then watch the npc run to the target without missing some of it. BTW, I used the thug in the test and 5 is the running animation for the thug; 40 is not.
Addendum:
The target needs to be dynamic but it can be invisible.
Addendum #2:
If you want the npc to run from one target to another and then another you will have to time the npc to see how long it takes him to get to the target. Then you have to use a timer so that it delays that amount of time for the npc to get to the target before you have him/her run to the next target. See code.
;Artificial Intelligence Script
;Header
desc = run to target
;Triggers
:state=0:etimerstart,state=1
:state=1,etimergreater=1000:settarget,settargetname=target1,state=2
:state=2:etimerstart,animate=5,movetotarget,state=3
:state=3,etimergreater=5500:settargetname=target2,state=4
:state=4:etimerstart,animate=5,movetotarget,state=5
:state=5,etimergreater=2500:settargetname=target3,state=6
:state=6:animate=5,movetotarget,state=7
:state=7:none
;End of Script
Download contains a zipped folder of an fpm and the script for it. Place the map anywhere you want and the script in the scriptbank folder.