As I finally managed to solve the problem i wanted everybody to know what was the reason.
I assumed the problem was behind the Admin username change, but that was just a coincidence. At the same time I installed server updates with Internet Explorer security patches. Something went wrong with these and Internet Explorer stopped working.
Because Blackberry Manager uses some kind of IE component to connect to MDS service it disallowed the BES management.
I removed the updates and reinstalled them. After this step all works without problems.
Thank You for help in solving the issue. Have a nice day
I will take into consideration the reasoning behind the BESAdmin user privileges. I'm afraid to break anything as it was set up by someone else (who I suppose knew what he's doing). After I receive proper training I'll have to apply all the ideas I got during this problem.