It could be frame rate syncing. Have you tried adjusting one of the two resistors near the caps? Mine are set to do about 500ms on - 2.5 seconds off, so it's a pretty slow flash. I am using this circuit http://www.friendlywire.com/tutorials/ne555/ with modified resistor values and I added a momentary push button to simulate a reed switch.

I have a working astable circuit that flashes the LED with the 555. I did put my LED in backwards at first, so check that. If it is a bug, it might be something related to how the LED's are being wired. A screenshot of my circuit with 6vcc power supply for comparison.