Open a support ticket with JJP. I had (have) a similar issue. You can bypass a light to test. Unplug the green and red wires frome the first bad led and hook them to the next in line. You also need to bypass the light in the software.
You should use the all white led test to trouble shoot.
I did all this to no avail. JJP support had me unplug and replug the small usb in the silver case. Also the big usb's behind the graphics card. That seemed to work for now.
Update. Issue is still present.