When adding masterserver to your server.cfg, and running HLDS, you might be seeing the message "Your server is out of date. Please update it." Well this can be removed if you update the server or download the latest one using hldsupdatetool.
Here is a solution
Download HLDSupdatetool, install it.
Open cmd from start->run. Go to that directory where you installed hldsupdatetool and type in
HldsUpdateTool.exe -command update -game cstrike -dir "C:\HLDS"
This will begin the HLDS download process in C:\HLDS directory, you can change it. After the download is complete, Run HLDS.exe to make a server.
Then you can patch it with non steam + steam, that is support for protocol 47 + 48 simultaneously. It will work fine. To download (free) the patch click here.