If you have custom sceneries, have you tried with your community folder empty or starting in safe mode ?. I am asking that because with one of my custom scenery ATC was always assigning the same runway whatever the wind direction was. I contacted the developer and he identified an issue, made a change and it fixed the issue with ATC assigning wrong runway.
If this is not the case and you are still having the issue without any mod installed, then there is an existing bug report where you can post your issue: