I know this is an old post, but I have the same issue as Timosoren. 2009 with no diode in D1, so I went ahead and added one...
I didn't find any cold joints or any other issues with the board, but when I plug it in without the housing, I can make LED's D3 and D4 flicker. I put it all back together and still have a dim D3 LED but after a couple days the clock still has the correct time.
Not sure if it was the taking it apart or adding the diode that fixed it.