foreach(@stack1){
    my $qq = pop(@stack1);
    print "$qq popped from end of queue\n";
    print "left on stack : @stack1 \n";
    print "stack size is $#stack1 \n";
}
[download]

You are iterating on @stack1 and, at each iteration, tou pop the last element from the stack. When foreach reaches the point where elements have been popped it stops.

You can try:

while(@stack1){
    my $qq = pop(@stack1);
    print "$qq popped from end of queue\n";
    print "left on stack : @stack1 \n";
    print "stack size is $#stack1 \n";
}
[download]

So your loop iterates until @stack1 is empty.