I recently bought a PS3 and whenever I turn it on, even with the controller, the controller always starts up as #2. This is hugely annoying as (for example) inFamous can only be controlled using controller #1. I have to manually change the controller over to #1 once I get into the game.
Because it's likely part of the problem, I should mention that I also have a USB IR receiver (built for the PS3) also plugged in, so that I can use my universal remote for things like BluRays and Netflix.