I can't speak to your exact problem.... but I have been tinkering with a Pi3 now for a few weeks. It is also set up with thread priorities, latest build, etc. In my experience:
1. If the Pi is "busy" such as importing, building thumbnails, etc. it can hiccup. Once it settles in it is fine.
2. Since the Pi's USB bus includes the network adapters, it can get bottlenecked fairly easily, causing buffering/hiccups. I haven't had good luck using its wireless for anything other than maybe MP3 playback. I recommend the ethernet port, not wifi.
3. Playing hi res audio works to an extent, but I recommend using a DAC that natively supports whatever bitrate you are playing. Make sure in MC your DAC is using a hw:, plughw:, or front: ALSA connection with no conversions. Converting bit rates on the fly can cause buffering/stuttering. Use only whatever DSP is necessary. I recently bought a hifiberry and it plays natively very well up to 192 KHz. I really like it.
4. I haven't found much difference whether playing from the Main Library, a server library, or as a DLNA renderer (if no conversion is used).
Keep an eye on the CPU usage during various routines, maybe you can figure it out. Playing 192KHz files natively uses typically between 10-15%. When that little CPU spikes up it can cause audio problems. It could be you are not experiencing issues playing to the IPod because it is down-converting, and the USB is playing full native format. You didn't mention what files you are playing or what the source is (network, attached drive, etc.). Keep in mind all the data in/out of the pi is on the same USB bus. Keeping the data bandwidth within reason helps.
Hope this helps.