I have been experiencing the same with this set of missions on both servers (CW and Test Server) when running co-op missions. (only host gets the PP award) It seems to be alleviated by running a solo mission after logging in, before running any co-ops. I'm not 100% if its the missions or the server configs but I suspect the missions at this point. Thanks for the info and keep me posted, I'll dig for the source of this problem.
edit: I think I'll set the draft radius back to zero as recommended by Karnak and see what happens... (will get rid of stray bugged base missions) - wait... the test server is on draft radius zero and I get the same thing... I thought it was a quirk of me being local to the server again but now that you have reported it too I suspect the missions (this never happened to me with EEK 2.1) I will double check all my settings to be sure...