Correct, not limited to Apogee. I have a Universal Apollo Duo, all worked great till I installed OS 10.9. Currently, I'm at 10.9.2, same issue. Stuttering, popping when playing back audio files in QT. No such problem in iTunes.
I always have my sample rate at 88.2, as that's the format I record in. No help. What works is opening my DAW (Cubase 7.5.2)! When I do that, QT will play, albeit with an occasional pop. Not perfect, but no stuttering.
This is totally uncool, and needs to be addressed LAST YEAR!
I'm almopst ready to eliminate QT for a suitable subsitute. What is "VLC" and if I;'m not editing video, is it suitable for music playback? Now, I just right click the audio file and select iTunes as the playback vehical.
Cheers,
RJ