I'm going to ask a few silly questions first, no offense meant.
Are you using a Yamaha Stagebox or are the inputs pugged straight in to the QL5?
Have you installed Dante Virtual Soundcard (DVS) on the computer?
Have you selected DVS as the "audio device" within logic?
Have you "patched" the inputs from DVS into each channel of Logic?
Answer these and I bet we can pinpoint what's happening.
Are you using a Yamaha Stagebox or are the inputs pugged straight in to the QL5?
Straight into the omni inputs on the back of the QL5
Have you installed Dante Virtual Soundcard (DVS) on the computer?
Yes. Both DVS and the Controller
Have you selected DVS as the "audio device" within logic?
Yes
Have you "patched" the inputs from DVS into each channel of Logic?
Yes. Patched and showing signal on everything except for the inputs coming in from the QL5 even though routed properly in the Dante Controller