I had to reorganize things a bit because (the only one) SPDIF input in my AVR was already occupied by optical connection to TV set (I use TV as a player for some streaming services) so I had to switch to eARC between TV and AVR first.
Then I connected Vu+ SPDIF output to AVR's SPDIF input (video over HDMI, audio via optical SPDIF) and the issue went away - theese messages are still there but no audio dropouts.
If HDMI connection (port in Vu+ or cable) was at fault then I would also have some distoritions/interruptions in video, not just audio. So not sure what to think about it.