I had the same issue yesterday. SQ6 with Firmware 1.2.2 and two DX168/X. Everything was connected before the power on sequence. The power on sequence was DX168-1, DX168-2 and at last the SQ6. The orange lights were flashing, in the routing tab I saw that the DX Link was established. But when I tried to route some signals to the output the Black/white square shows me that the output is not available. I simply disconnected and reconnected the SLink cable and the I it works fine. It seems that the initialization of the stageboxes on power up was not completely done by the SQ.
There is also another issue, maybe it is one by design. In in the output routing tab of the SQ I have to rout the output sockets 1-8 for the first DX168 and 17-24 for the second one. the output sockets 9-16 always are displayed as unavailable.