Oldbayrunner:
You can remove it manually by clicking on the flag in the top right box in the game screen.
Right, and this ain't necessary when putting from the green, because the flag will be pulled the second you release the putt.
What we see in the putt replays is only a virtual image of the virtual flag.
As a guess, the "blind" putting may be the consequence of disorder in the system. Clearing the Flash cache might help.