Yes I get the invisible flag(s) from time to time.. seems to happen mostly on Merion for me.. what I do know also is that when it happens to me, it is happening to others at the same time, which indicates it is not a problem with my browser / flash version / hardware geometry..
One time in a skins game everyone confirmed at the same time when the flag had disappeared.. if it were just a machine / browser / hardware fault, then we wouldn't all be seeing no flag from different parts of the world at the same time..