To be honest I'm not sure what exactly solved the issue but it seems that removing /Library/Application Support/com.apple.TCC/TCC.db file and restarting the system solved the problem, at least this is the last thing that I've done.
In addition, I added r/w permissions to everyone to /Library/Application Support/com.apple.TCC/ directory.
Many thanks to miatamania and all for your help and support!