Can't remove waypoints

[Palut]

When generating missions for my campaign on the Stalingrad map I'm unable to remove waypoints.  On the briefing map I can right click them and delete them, but once I make any other selection they come right back.  I can delete them then immediately go into the game and they are back.  

 

Changes in altitude at each waypoint will not carry into the game either, they are simply ignored.  Am I missing something here?

 

Any help would be greatly appreciated!

[benchedgamer]

@Palut I would suggest going to the New Issue thread: 

 and posting the issue there. I do have the same issue but wont be able to post the campaign file until later tonight.