There are a few things that you should check. First, check that all of the LEDs are facing the same way. There is a “collar” around the base of each LED, on which is one flat facet. Check that all of those facets are facing the same way.
The charlieplexing scheme for the Bulbdial is described in some detail in this article:
http://www.evilmadscientist.com/2010/on-the-design-of-the-bulbdial-clock/
http://www.evilmadscientist.com/2010/on-the-design-of-the-bulbdial-clock/
Each green LED is connected between one of LED1-LED6 and one of LED7-LED9. Check to make sure that all of R1-R10 are inserted properly, and to make sure that there are no accidental connections between the LED lines– you can check at the vertical jumpers. You may also want to read the detailed schematic, to trace between the microcontroller pins and each of the vertical LED lines, to make sure that the correct amount of resistance is between them.
