[popcornmix]

Very recently, I tried enabling Sync Playback to Display: PLL. After just a couple hours of use, I haven't seen the problem return with this setting enabled. I was under the impression that this setting was unnecessary with audio passthrough, and I'm pretty sure I didn't need it with my CuBox i4pro. I don't even know exactly what it does, since the PLL setting isn't explained on the wiki.

Is this a known problem? Is the PLL sync method a reliable fix? What does it do?

A media player always needs a mechanism for correcting sync between video and audio, either from errors in the file, or because video and audio run off asynchronous clocks (which they certainly will with USB audio).

The preferred solution is to resample the audio to speed it up or slow it down a little (typically it's < 1%) until the audio/video are in sync. It may cause a slight warbling sound (especially at the start of a file).
With passthrough you can't resample. The default option is to duplicate or drop samples. Depending on the receiver, that may produce an audio glitch (some receivers are quite good at masking it though).

The Pi has an additional solution to this which is adjusting the PLL (clock) of the HDMI display. This allows audio/video sync to be corrected without audio warbles and it works with passthrough. If it works for you it is the best solution. Unfortunately some TV/receivers don't like the clock ajustment and you may get audio or video dropouts. Most are fine with it and if this is the case you should use it.