My guess is that this is not a problem with either the remote or the IR receiver. It appears that button presses are seen by the STB but the processing is delayed. This causes untold grief when scheduling a DVR recording or just trying to navigate the IMG in real-time. It's likely a problem with the priority to which the embedded SW in the STB manages user interactions. These boxes have a lot on their plate managing ongoing DVR recordings, current channel buffering, etc, but that's no excuse for poor performance. They need to have enough horsepower to keep up with everything including being responsive to user input.
The problem everyone is missing is that Comcast HD DVR does not have this issue. So while we can say oh poor performance on the STB or the remote. it seems the issue is only the equiptment FIOS is using. Maybe they should look up the hardware specs for Comcast and see why Comcast has no issues with DVR HD remotes and programming guides?
I am having this same problem but the weird thing for me is that if the tv is off the remote and stb work everytime on every click. When I turn the tv on it hardly will work or change channels which is very frustrating. I have tried resetting the box but doesnt help. I called verizon and they sent me a new remote which didnt help. Any ideas? Oh , the stb is the Moto QIP 72161 and the TV is a panasonic plasma.