iterate through array of objects with lists of objects

I need to iterate through an array of objects, each of these objects holds multiple generic Lists of objects. The purpose is to compare a specific object with the contents of the generic lists and to remove it from the 1 list it exists in (it really only does exist in 1 list).

The problem is, when i try to remove the object from the list in question, it removes each object of the same type (by Tag) from each array object's list, and not just the "one".

Each object in the arrColum has a script called Check, which contains multiple generic lists of objects.

This is the script is use to iterate through my array of objects with Lists:

 var arrColum = new Transform[8];
 function RemoveFromColum(theObject : GameObject)
 
 {
 for (var colum : Transform in arrColum)
         {
             
             if(colum != null && colum.gameObject.active ==true)
                 {    
                     var checkScript : Check = colum.gameObject.GetComponent(Check);
                 
                 if(theObject.transform.tag == "Cube")
                     {
                         var theCubeList : List.<GameObject> = checkScript.cubeList;
                         RemoveFromList(theCubeList, theObject, colum.gameObject);    
                     }        
                 }
         }
 
 }
 
 function RemoveFromList (theList : List.<GameObject>, theObject : GameObject, theColum : GameObject)
 {
     var index : int = -1;
     var checkScript : Check = theColum.GetComponent(Check);
     for (var curr : GameObject in theList)
         {
             ++index;
             if (curr.transform.GetInstanceID() == theObject.transform.GetInstanceID())
             break;
         }
     if( index >= 0 && index < theList.Count)
         {
             theList.RemoveAt(index);
             checkScript.columCount-=1;    
         }
 }

Can anyone point out what I'm doing wrong here. Or suggest a better/quicker way of achieving this properly?