5A-75E V8.0, pinscan can drive all LED pins, but my program can only drive some pins?

[cdwijs]

I've been working on documenting my 5A-75E V8.0
I can compile and run pin-scan [1] on the board, after specifying my FPGA has a CABGA256 package. Then all the pins on the LED connectors are driven, and I can check those with a serial to USB converter.

Next I made a .lpf file, and a verilog program to let each outputs blink in an unique pattern [2]. After setting output enable (FPGA pin M4) to 0, I can drive about half of the outputs on the LED connectors. I have not been able to drive these pins:
J1 pin 3
J1 pin 8
J1 pin 12
J1 pin 14
J1 pin 15

J2 pin 3
J2 pin 8
J2 pin 12
J2 pin 14
J2 pin 15
(and a lot more, see top.v [3] for the full list)

What am I missing in my multiblink program?

[1] https://github.com/cdwijs/chubby75/tree/colorlight-75E-V80/5a-75e/pin-scan
[2] https://github.com/cdwijs/chubby75/tree/colorlight-75E-V80/5a-75e/multiblink
[3]https://github.com/cdwijs/chubby75/blob/colorlight-75E-V80/5a-75e/multiblink/top.v#L14