The positive end of the LED should be connected to Pin 3 of the timer and the negative ends need to be connected to ground right? If so I have it set properly, the Dev told me that the frame rate scaling of the LED ends up syncing with "off". Mine is based on Ben Eater's circuit .

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.

Thanks for the response! After some trial and error I think the issue is with the yellow LED specifically. My clock module will have a Flasing LED if I change the color to blue but it won't flash at all for