[asavah]

PS before ffmpeg bump it was perfect.

Can you confirm the actual nightly build?
i.e was #410 perfect and #411 is bad?

Can you reproduce with a file (e.g. a recording) played from file interface (rather than PVR)?
I'd like to be able to reproduce the issue here (I haven't heard any audio issues myself).

Does disabling "sync playback to display" avoid the issue?

I'll try to reproduce with this builds and report back shortly.
Disabling "sync playback to display" makes it a little better, but still not perfect.
It's like tiny little clicks, I can't hear those clicks when watching same source on my desktop with eg. VLC while using same headphones, both pi3 and my desktop are connected to hdmi of the same display and headphones are connected to the display audio output.
I can't reproduce this with files, and I'm not using PVRs, live tv urls are provided via my own addon (python winxml) which parses ISP's playlist and feeds the urls to Kodi.
Urls look like udp://@239.0.19.20:1234
If I find a file sample which reliably reproduces the issue I'll post a link.