I placed markers into the program as Console.print() statements to track the integers it was sending to
lcd.setCursor(orderCols[k],k%cols);//move cursor to xy
lcd.write(LCDarray[k%cols][orderCols[k]]);//write LCDarray[y,x]
These are the values it gave me... I don't see any problem with the values.
It alternates between 0 and 1, oh... damnit I know what the problem is. I'm not tracking whether I printed (0,7) or something twice...
So I print the same spots more than once a random number of times... 
0,7
1,1
0,9
1,5
0,9
1,0
0,8
1,13
0,12
1,13
0,6
1,10
0,12
1,6
0,3
1,14
0,7
1,11
0,15
1,4
0,14
1,2
0,11
1,8
0,2
1,0
0,5
1,4
0,10
1,15
0,1
1,3
So that's the problem solved, now to find a way to implement that and still get my random numbers.
I guess I can generate a multidimensional array of 1-16.