Arrow,  
  
First off, could you confirm you use KMD v 1.07 (Menu ? / About KMD...) ?   Because what you described is little bit weird. There is no way to "unchek" Player if you have only one flight in your mission. By default the first flight is for the player.  Secondly, if you check "Take off" and your flight doesn't have at least one waypoint, it will show you a msg box telling that there is no airfield to take off from. And that won't "uncheck"  Player... 
  
 
  
Wingmen must be on the same flight as the player (like in real life   ...).   So if you set the flight size to 3, you will have 2 wingies. 
  
 
  
It's a game engine limitation. You cannot have sereral Flight starting on the same Airbase on the same time. So if you want your flight 2 to take off form the same AB, you have to delay it (5mins or more. It depends of the size of the player's flight).  
  
Hope that will help you...