[fysiks]

In your original post you say "when HLDS starts" and "after server.cfg". What does this mean? Server.cfg is executed when the server starts.

I don't use the Windows version of HLDS so I'm not entirely sure how the GUI configuration applies to the server or if there is something different with how it works compared to Linux.

It's hard to understand what you're saying with regards to what is happening and what you did. If you want 2 minute rounds, set the value to 2 minutes in both places just to make sure it gets set. Is there a reason you don't just do this?