For those that have noticed some servers are not displayed in the Steam Server Browser the most likely cause is the "Working Directory" from which the server is running from.
Most providers and clans using Dedicated Servers use the server management software TC Admin but this issue would apply to all methods of launching server including a simple .bat file.
The Working directory MUST be the Binaries folder. In TC Admin it is in the Service Settings / System Settings depending on where you look (TC Admin requires both, System changes future game installs and Service Details is for currently installed instances). The same goes for other applications for which I am not familiar so refer to that programs documentation of how to change it.
In a .bat file, if the file is not located in the Binaries folder you will need to change it using command line entries. The way to change the working directory in .bat files is to simply use "cd <PathToBinaries>".
Using the full path to AA3Game.exe in a .bat file or other application does not change the working directory. Windows uses the "Currently Active" folder from where you launch a command as the working folder so you must define this properly.