This might sound a bit stupid but something is wrong. I can't even drop waypoints. If i click on the map with the mouse buttons it switchs levels.
The controls are all set to defaults.

I have the gold edition( raven shield and athena sword) Raven shield is patched up with 1.60 and atehna patched with the latest too.

A little help would be appreciated

Ok nevermind guys i fixed the problem.
I needed to put the AA in tray tool and CCC at application controlled, go figure....

Sorry but I'm having the same problem you had. When i try to lay a waypoint, it pops me up a floor so I can't plan any of my missions. I'm not entirely sure what you're refering to when you said what you did to fix it, can you explain it to me? Thanks a lot.