LOL the code's too complicated. It's a simple problem so the code should be simple too. Elegance is important in programming. There's also a lot of repetition in your code. Repeated blocks of code should be made into a function. This is the "do not repeat yourself" principle. Have a look at how small my python code is:

from collections import deque

def read_queue():
    return deque(map(int, input().strip().split()))

nstacks = len(input().split())
stacks = [read_queue() for i in range(nstacks)]
heights = list(map(sum, stacks))

while len(set(heights)) > 1:
    ihighest = heights.index(max(heights))
    heights[ihighest] -= stacks[ihighest].popleft()

print(heights[0])

Edit: made the code a bit more elegant.