I posted recently about a similar problem with QC. I use an Innuos Pulse with a Bryston BDA3. The BDA-3 uses mechanical relays to switch resolution to preserve SQ but there is an inherent delay. With Sense, there is a setting to adjust for that, but with QC, that setting is bypassed. As a result, the beginning of songs gets cut off or stutters.
I've worked with both Innuos and Bryston support about this. Innuos determined that QC bypasses the Pulse internal player and doesn't allow the built in settings to work. Bryston acknowledged the issue and is working on a fix.
It seems that QC is more compatible with some setups than others. I've stopped using it. Hopefully future firmware updates will address the issues.