IIRC the only two files you need to have on the server are:
UT3Bots.u
UT3BotsPathing.u
On my Linux dedicated server, these files go into:
/opt/ut3-dedicated/UTGame/CookedPC/
Then you need to specify these mutators in the server startup script.
The Unrealdecoy server is running with a command line that looks
something like this:
ut3-bin Server DM-BioHazard?Game=UT3Bots.BotDeathmatch?GameMode=0?
<snipped a bunch of optional params>?
mutator=UT3Bots.ServerMutator,UT3BotsPathing.PathNodeMutator
Of course, file locations will vary depending on whether you're
running it in Linux or Windows, and whether you're running a dedicated
server or using the UT3 game client.
If you still can't get it running, I have a dedicated Linux VMware
image (compatible with the free VMware Player) that should work right
out of the box. Email me for a link if you need it.
-Warf