Boolean set to true, false in Update() function because of Start()

I am having an issue where I set a boolean value in one function and is being overwritten by the time i need to use it in another function. For context, this is an NPC Core for a game I am developing. The player has the ability to set any of the pieces to start first (which subsequently can also be an NPC) and that is where my problem occurs. here are the scenarios:

Scenario 1 If a Player piece is selected to move first, everything works fine and the following pieces, including NPCs, all work properly.

Scenario 2 If an NPC piece is selected to go first, the NPC never moves because StartWait is still false for whatever reason.

Using Debug.Log and a little bit of debugging knowledge, I have tracked the issue down to being this. In scenario 2 from above, after I set the boolean, it appears Start() is running and setting the variable back to false. I know this because the output in the console says "Waffles Toaster" instead of "Toaster Waffles".

How could I go about correcting this so start does not override my previous assignment?

 // Initialization
 void Start()
 {
     Debug.Log("Toaster");
     NPCCoreVars.Timer = 0f;
     NPCCoreVars.StartWait = false;
     NPCCoreVars.ChosenPiece = null;
     NPCCoreVars.ChosenCell = null;
     NPCCoreVars.MoveOperation = 0;
     NPCCoreVars.CurrentNPCTeam = TeamChoices.None;
 }

 // Used to control the timer
 void Update()
 {
     // Are we waiting?
     if (NPCCoreVars.StartWait == false) return;

     // Decrement the timer
     NPCCoreVars.Timer -= Time.deltaTime;

     // Have we passed the timer?
     if (NPCCoreVars.Timer <= 0)
     {
         // Reset timer variables
         NPCCoreVars.StartWait = false;
         NPCCoreVars.Timer = 0;

         // Call the move function
         DoNPCMove();
     }
 }


 // The core function that decides what piece moves and where
 public void NPCMakeMove(TeamChoices NPCTeam)
 {
     ...
     if (NPCCoreVars.ChosenPiece != null && NPCCoreVars.ChosenCell != null)
     {
         NPCCoreVars.Timer = 2f;
         NPCCoreVars.StartWait = true;

         Debug.Log("Waffles");
     }
 }