Problem with PS3 remote and controller not staying synced up with console

[DrasticPlastic]

I play a lot of guitar hero 3 on my ps3 and use either the remote or the console to turn on the PS3 so that the guitar will be set to controller #1. Sometimes when watching a blu ray or dvd on the ps3, the remote will work just fine at first, but at some point during the movie, I try to use the remote to pause the move, or hit the display butotn to see how much time is remaining, but nothing works. If I turn the guitar controller on, it works fine, but I can't really use that to well, nor do I want to, for controlling dvds. Sometimes even if the console is off the remote won't turn it on, and if I grab the controller and press the PS button, the four led lights just flash and nothing happens. What causes this to happen so often, is it something to do with me using the guitar controller so much? I've checked the batteries in my remote and controller and they are just fine, so I know it's not low batteries causing the problems.