If you're not using an RF base station (MRF-250, 300 or 350) with the remote, look in the RF Settings in the software and make sure that it's set to "IR" for each device. It's unlikely that it would be set to RF (that's not the default), but check it anyway. If it's correct and you also have the correct IR commands assigned to your devices, it should work fine. Otherwise, there is likely a problem with the remote.

Mike
www.SurfRemoteControl.com