===== Why doesn’t a squadron get allocated to do a mission for which it has the same preference as another squadron which __does__ get allocated to the mission? =====

Probably because of its preference for the mission for which it __does__ get allocated (as generated by the allocation linear program).  Here’s a simple example:

^Preference   ^You         ^Me^
|1	      |Vanilla	   |Vanilla|
|2	      |Chocolate   |Strawberry|
|3	      |Strawberry  |	|

We have 1 pint of vanilla ice cream, and 1 pint of strawberry.  We both favor vanilla first, but since my preference (#2) for strawberry is higher than yours (#3), I'll get stuck with my second choice & you'll get your first choice.

  * Option 1
    * You:  Vanilla (#1)
    * Me:  Strawberry (#2)
    * Sum of preferences:  1 + 2 = 3

  * Option 2
    * You:  Strawberry (#3)
    * Me:  Vanilla (#1)
    * Sum of preferences:  3 + 1 = 4

To minimize the "cost" (the sum of the preferences), you get vanilla, I get strawberry.