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.

Don't give up. It is worth figuring it out. My personal favorite out of 9 games. For about three weeks I have been trying to figure out what was going on with my light issue. Tonight I think I have solved it. Make sure you check not only your lights but the cables. I was bypassing a light that was giving my trouble but still had problems. Turns out I was using the same cable. One of the wires was loose on the connector. I feel pretty confident that will fix it.