I would leave the wires as they were originally as this looks the correct way, But i reckon some one has put the diode on incorrectly . And if one is wrong i would check all the others just in case. And check or renew/ resolder the header pins on the cpu as this causes switch problems

Once I get these problems sorted the boards are all going of to Beaky as all of them have all manor of hacks preformed on them. I'll replace the connector here also so hopefully that eliminates any problems there to.