Reinstalling polkit fixed problem with setuid bit. Thank you for that!
I have checked history and I wasn't able to find any command which consisted polkit or pkexec words. So not able to explain why it happened to me.
Ok so that part partially is done. How about mirror list. After choosing and saving a few countries shouldn't them be again checked in next approach of modification? By that I mean that after opening a list I see:
and it's always the same. Why I don't see Germany, Latvia, Austria, Switzerland etc marked down as well, while those countries was previously assigned? Or my understanding is wrong and that's correct behavior?