If you google the topic "plasma TV interference with IR remote" you will find tons of info. Turns out plasma TVs and even some LCD TVs spew out non-visible light noise in the infrared band. This can result in either a non-responsive IR remote or unpredictable responses.
I'm posting this because I know of at least one documented case where one of our customers was having endless issues with our V2 board and Apple Remote. Turned out as soon as he turned off his plasma TV/monitor the problem went away.
Apparently this problem can affect a wide array of IR controlled devices from multiple manufacturers. It's not a defect of IR control. It's a defect of the TVs.
So this is a heads up that in case you're getting flakey responses or no responses to your Apple Remote with our preamps, turn off your TVs and other display. Doing so will likely solve the problem.