I have started getting a crackling/pop sound from my E50 that's about 1 year old.
My chain is: Apple TV -> HDMI -> Sony TV -> Optical out -> E50 -> RCA out -> Yamaha S-A501. and
Coreelec on a Odroid N2+ -> USB -> E50 -> RCA out -> Yamaha S-A501
The sound will occur in several different ways:
1. If the E50 is turned off before the Yamaha I get a loud pop/crackle
2. If I play a MQA song from Tidal via Coreelec I will get a crackle sound at the start of the song
3. If the input switches bitrate I get a crackle on the start and end of the change
4. If I switch input I will get a crackle.
I have unplugged the USB or Optical with the same results. If I plug the Optical into the Yamaha, I don't get any crackling. It returns if I introduce the E50 back into the chain.
Note that the Apple TV, Odroid N2+ and the E50 are plugged into a quality UPS.
I am getting disappointed in Toppings products. I had to return a PA5 twice before getting the Yamaha as a replacement. Now the E50 too.
that pop/crackle is a normal response to an element on the audio chain losing power, as for your point number one, that one is on you, speakers are the first thing you should power off in a chain (and last one you power on too).
regarding point 2 - 4 . what you describe seems to be a case of the device stuttering when changing sample rate. me and a lot of people had this exact problem with the tempotec sonata hd pro, while trying to play bit perfect mode/asio, and for most of us it was fixed by a firmware update. what I don't quite figure out is why it started happening to you after a year instead of from the beginning.
did you change something in your system near the time when you started noticing this? for instance the power source for the E50, or maybe could you have changed something in the settings of the signal source device which had an effect on the behavior of the sampling rate (you might have been resampling everything until now, and recently start forcing the device to atempt bit perfect playback)
it seems to me as if your issue is related to MQA playback or its software, I figure this because you mention you don't get this issue when you plug the optical directly into the yamaha (I think optical will not send true MQA, so the Yamaha should always request a resampled stream and only take that), plus the correlation between the fact that I have never encountered this issue on my E50 and that I have never tried to play a MQA file
my advice is to try to turn off the auto stand by setting, to see if that helps . if it doesn't try to execute a factory reset, the instructions are near the end of the user manual