Using the ob-board i1 device for color calibration on the L2 machines can be a bit of an iffy proposition in my experience. I have seen it work properly, and I've also seen it fail in sending the data back to the RIP.
Onyx Media Manager (in this case) must be properly configured to communicate with the on-board i1 device, and the Media Manager software must be ready (on the right page, and waiting) to receive the data at the proper time, otherwise the communication will time out and the data will be lost. It sounds like that is what is happening in this case.
When possible, an external measurement device is preferable for the L2 machines in my estimation. HP has dramatically improved the ability to synchronize medias and ICC profiles with the RIPs on the L3 machines.