He just stands there. If I can even get the waypoint to show up. It seems to work fine on a new empty level, but none of my in-progress ones.

are these previous maps old ?

Try re saving one under a new name then try again

old? I tried saving under a new name but still have this problem. I also can't get the waypoint to show up at all more than half the time, and if it does, it'll be on top of a random mountain not anywhere near the center of the screen when I hit "create waypoint".

He won't move

create the first waypoint marker in Topdown mode, then you can add others in free flight mode.

Are the any trigger zone markers that appear twisted or are not flat.

Pressing M on the keyboard hides and shows the markers.

Now if the AI and waypoint are more then 600 units from you, then they wont move till you get to that distance.
Try setting the soldier to always active. see if that helps.

Waypoints and ai work fine on a blank slate but they break as soon as I put them by entities, making level creation impossible.

I am not having issues on my machine with waypoints or AI on them. There range is quite short from the default script.
Set the always active to yes in properties panel for them to have them active within 3000 units of you instead of 600.

Now only the soldiers will pace the waypoints, it is the way the scripts are setup.

Other characters can be scripted to use waypoints, but you will need to match the animation calls in the FPE file or totally modify a script for your needs.

Now also these guys need a little bit of room around them at least 4 ft, better around 8ft for most cases, so they don't think they are trapped in a boundary.

Which soldier is that pictured above?

I'm having the same issue. Took the suggestions of Pirate Mike, all but the modifying of the scripts, and it just is not working. Would the specs of the users computer influence this problem?

Should not. Only thing to do would be to try a file verification and be sure all the files are download proper.
Which soldier, and which script did you modify?

Ok the fix for Corvus's map was the the forcesimpleobsticle=3 was not in the fpe files of the entities from the warehouse building pieces. adding that statement in the orientation section, saving the file, and erasing the dbo and bin files and reloading the level works on my machine.

So in the metrics mode in test game there is a slider called debug. Setting it to 10 will show you the collision for the objects, ensuring that the path it truly clear for the AI.

How do you do a file verification?

Go to your steam library and right click on GameGuru...Select "properties" .....then select "local files" and finally "verify integrity of game cache"
See if that brings anything to light and fixes your issue ...

@FabledFoe: Did you get this going?

Sorry, was busy--Yes, it worked like a charm. Thank you, thank you both. +110. I didn't know we could even do that until now. Very cool.

Excellent. Glad to hear this.

Thanks