Mailtraq is fully compatible with Windows Server editions - but you may need to resolve some 'conflicts' with the default services Windows provides.
There are two likely conflicts:
Windows provides IIS - Internet Information Service - which is normally installed by default - to host websites and provide a basic message service using the Simple Mail Transfer Protocol (SMTP).
Mailtraq will now be providing the SMTP services for the server - so you need to 'turn off' Windows SMTP service in IIS.
If you are not running a website from the machine then you should completely 'turn off' IIS. If you are running a website from the machine, just stop the Windows SMTP service - and read the note at the bottom of this page.
Web Server in Mailtraq
Note that Mailtraq also provides a full web server as part of your Mailtraq Professional License, so if 'all' you wish to use IIS for is to serve a regular website, you can use the built-in webserver - read more here.
W2008
Access the Windows Server Manager by going to:
Windows Start | Administrative Tools | Server Manager
1. Stop just the Windows SMTP service
Go to Windows Start | Control Panel | Services
and select Simple Mail Transfer Protocol (SMTP)
Then click the 'Stop' link in the left column.
This will stop only the Windows email service so that Mailtraq can replace it.

In order to make this action permanent, open the Service and set 'restart' to manual, otherwise when you reboot IIS-SMTP will restart.
2. Stop Windows IIS Admin Service
Go to Windows Start | Control Panel | Services
and select IIS Admin Service
Then click the 'Stop' link in the left column.
This will stop both Windows mail and web services so that Mailtraq can replace them.

In order to make this action permanent, open the Service and set 'restart' to manual, otherwise when you reboot IIS will restart.
Intermittent problem
One service - one port
Running a web-site and webmail on the same server. HTTP services (i.e. a website and webmail) run by default on Port 80 - but you may offer only one service per Port. So, in order to resolve this conflict you will need to change the port that Mailtraq offers webmail on. This is explained here.
You may find that you sometimes have a problem with Port 80, but after a reboot it will work fine, then fail at the next reboot... and so on.
The reason is that Windows starts services in an arbitrary order, so on start up there can be a 'race' to see which program or application gets the port first: sometimes Mailtraq will win, other times not.
Tip:
If you need to discover which ports are in use by which program then you can use CurrPorts (32-bit or 64-bit) or a similar utility to view Process Services and Local Ports.
Or enter the following from the Command Line.
netstat -aon -p tcp
which will list all listening and connected TCP ports and will list the PID (process) using the port. You can then discover which PID relates to which process/program by adding the PID column to the Task Manager.
Windows 10, Vista and higher, W2008 and higher
You need to run the command prompt as administrator. You can do that by right-clicking on "command prompt" in the start menu and go "run as administrator" otherwise it is only run as a limited user.