[avoidconflictz]

I'm starting to think that, since nobody else reports this, it is caused by the AVR. The only solution to this is to disable audio passthrough ability for Dolby+ under System -> Audio settings.

Have you considered upgrading firmware in your AVR? I´m really thinking about it. The last thing I´m going to try is KODI under Windows, if the problem is there as well.
I tried to read the debug log. From what I understand (probably not very much) is that both - the first successful attempt to play the file with EAC3 and the second unsuccessful (3rd file to play) - look the same. No errors and no difference. So it either doesn´t do what it says in the log or it does and the AVR can't process it. Damn I wish I could try it with different newer AVR, but everybody I know has the older AVR without HDMI.