Virtual Playback not working after 1.6.0 upgrade

We have an SQ6 that was running FW 1.5.6 and using 28 channels of virtual playback with Apple Logic over USB cable. After upgrading to FW1.6.0 and using the same virtual playback file, everything works fine except the first two inputs on the SQ. We are mapped 1:1 from Logic to SQ. When routing output 1 & 2 from Logic to SQ there is no input signal. If I route Logic 1 & 2 to any other SQ input, the signal is fine. Have verified Logic is sending audio. It seems to be an issue with USB inputs 1 & 2 on the SQ. If I route any other channel from Logic to inputs 1 or 2 on SQ, there is no signal. Any thoughts on what’s happening? Any known issues? Possible bug with 1.6.0?

Just to be sure:
But you’ve also on the SQ patched your USB channels 1-28 1:1 to the desired input channels ?
So isn’t it possible that your USB 1/2 might still be patched to input channel 47/48 as standard?

All routing verified 1:1. As I mentioned, this worked perfect with 1.5.6 and I am using the same Logic file and same SQ file. Only difference is the SQ now on 1.6.0 FW.