Problems with IR transmitter

I currently control all my AV equipment using an IR receiver that is attached to the TV and transmitters located in the AV closet. This works fine for all my components (receiver, DVR, DVD player, etc.), except for some reason my new Apple TV will not accept signals from the IR transmitter. It will only accept them if the remote is pointed directly at the unit. I've tried it with transmitters that work on other components, so the transmission seems to be fine. Has anyone else run into problem or are there any ideas for solutions?