If your TV has an SPDIF out port, could you try to connect your HT with that bypassing the box ?? I never used the SPDIF ports of the box & always connected the Toslink optical cable from TV to my Logitch Z5500...I personally didn't find any sound issues on Xstream box myself...I tried connecting the optical cable on the box too but preferred to have it connected on the TV itself as the sound comes same from the TV's Optical output & the Xstream box's SPDIF output plus I watch movies daily from my laptop to TV by Miracast/WiDi & I don't even turn-on the box because it's not needed that time, so everytime disconnecting & reconnecting the Toslink cable from TV & the Box is troublesome for me...
If your TV doesn't have an SPDIF out port, then unfortunately you will have to rely on the box only to pass the audio to your Onkyo...
I am not sure why you are facing such sound issues with the box because I am not finding any such issues on my setup...