Update / Edit: Did some more troubleshooting. Turns out it was something very simple and stupid that was causing the clicks and pops. The HDMI to audio converter had a switch on it. The switch was for 5.1 audio, 2 channel audio and pass through. I switched the adapter to passthrough and all the clicks and pops went away. It was a hardware issue, not a software issue.
Raspberry Pi 3B running Rasbian OS. Ethernet wired in. Plexamp 4.2.2 headless.
I am every now and then getting random clips and pops in the audio playback. More often happens at start of track and at the end. But it does happen in middle of some tracks. I get like clicks or pops as if it was a record pop/click.
I have pulse sound server as my output because it is the only one that works with my Rpi for some reason. No matter what other output I try it only works for pulse audio. I am using the HDMI out for audio to a HDMI to audio converter for headphones. I have been trying to figure out what the issue is but keep scratching my head. I have tried each setting of sample rate matching and the pops persist. And every now and then at about 15 seconds at the start of a track I get a brief 1 to 2 second pause in playback.
I have turned off loudness leveling, preamp, limiter and still the random clicks and pops happen. I only have EQ, and SweetFades on. Cause come on now, I can’t be without my sweet fades and a bass boost. 
I set the cache to lowest, I also set the track cache to next track only.
Anyone have any ideas? Am I missing something simple?
Files are AIFF files, 44.1, 16bit, 2-channel stereo.
