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So, we had the same problem. I don't if this will still help you, I just found your question. And to solve my problem, I searched the web as well, but unfortunately, did not find a solution (at least in my quick search). So, what I did to solve it, I was just winging it.
Hope you'll be able to reproduce this. Run dbeaver Step 2. Select new connection type, in your case, MS SQL Server - Microsoft Driver - Next. When I did my config, the JDBC URL, Port, and Host were already filled out. So, what you'll be just doing here is to enter your User name and Password for SQL Server.
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Then, click Test Connection. You'll be prompted to download the drivers, do it. I did not do anything here. Just click Next Step 5. I just clicked Finish here. You're done, you should see the DBeaver - General Window. You can now access your SQL Server.