I have done a quick check on linphone_filtered.log and as far as I can see I have packages installed which provide all of the files and libraries except those ending so.avx2. That is surprising because I am runing on a Haswell processor and have libmkl-avx2, libmkl-vml-avx2 and all the other lib*avx* packages installed.
But none of them seem obviously connected with the black rectabgles replacing all the icons. So probably I have filtered out the relevant parts of linphone.log. I will try to look there maybe tomorrow.