Wii won't recognize my remote

Okay, so I have two remotes... And a third remote hooked up to my Zapper. I was playing Metroid for a bit, and then decided to switch to Medal of Honor Heroes 2 (which I use my Zapper for). But for some reason, the system wouldn't recognize the remote that is in my Zapper. The remote just flashes blue for a couple seconds and then shuts down. And it's not the remote's fault - I just used all three remotes in Wii Sports to see what would happen, and they all worked fine. But for some reason this one remote won't work on its own.

So... What's going on? Are like, the remotes synchronized in a certain order? In other words, can only the first two controllers you sync to your wii be used to start the system up and stuff?

I re-synched them all... And it seems to be okay now.

I THINK the problem was that I did that "disconnect" option that you can do by pressing the "home" button, do you guys know what I mean? And then it says "Press 1+2 on the remotes in the order of blah blah"... So, I'm thinking... Maybe I accidentally UN-synched my remotes by doing that. I only did it because I thought that's how I could turn off my one remote so that I could then switch to my Zapper remote... But I guess all that does is re-set your remotes, and then you have to re-synch everything again... At least, that's what it seems like to me. Am I right?