Occasionally it seems that even with the excellent cables provided with the Pixhawk 2.1 - you'll need to make a special cable.

9 of the connectors on the top of the Pixhawk 2.1 are JST GH connectors

I didn't see specific part numbers or sourcing for the plugs - so I'm posting it here.

There are 4,6, and 8 wire sockets.

Here's the part numbers (JST, then Digi-Key) for the mating plugs:

4 pin - GHR-04V-S      455-1594-ND  ($ 0.0928 ea in 25 qty)

6 pin - GHR-06V-S      455-1596-ND ($ 0.1296 ea in 25 qty)

8 pin - GHR-08V-S      455-1598-ND ($ 0.144 ea in 25 qty)

Crimp pins -- SSHL-002T-P0.2       455-1606-1-ND  ($ 0.0649 ea in 100 qty)

I have a hand-crimper on order from Amazon - if it works I'll post the results here.

KenMc