Well I have Mas 90 running on Windows 2003 no problem. Since Mas 90's workstation client seems to just be dependent on reading and writing to the shared directory, all you need to do is make sure domain permissions are correct. Also if for some reason you have slow performance, SMB Signing may be the culprit. This is enabled by default and is a security feature against man-in-the-middle attacks but turning it off, although decreases security a bit, should increase performance a fair amount. Usually with Windows 2003 the main caveats apply with any network dependent program, that being permissions and DNS. Other then that you should be fine. If this is Windows 2003 Small Business Edition than you may want to go through and disable unneeded services also. Unlike Windows 2003 Standard and Enterprise, small business edition by default has many services running and enabled. As a security and performance issue you may want to verify that only the services necessary are running.
-Adam