Remote Control no longer works

Sometime in the past year, my apple remote stopped working with my Macbook Pro. None of the buttons work 99% of the time. It used to be that just clicking the menu button on the remote took me to Frontrow, but this doesn't work anymore. Once in a great while, I'll test the remote by pushing the menu button, and Frontrow does start (1 out of 20 times maybe). But after it has started, the remote goes back to not functioning.
The remote itself seems to work fine: I used the camera to see the IR signal flashing, and pushing any button on it always wakes up the sleeping macbook that's sitting across the other end of the room.
The IR receiver on my macbook pro also appears to work fine: I took the MBPro to an apple store, where they booted up from an external harddrive and had the apple remote work just fin.
So the problem appears to be localized to a software issue on my macbook.
I'm not sure what software I've installed since it stopped working. The biggest change was an upgrade to OSX 10.6 from 10.5.
The only hint I have that some piece of software running in the background is interfering is that when I turn on Hulu Desktop (which I used to use with my apple remote all the time with no problem) I get a warning that says "You appear to be running another third-party application that utilizes the apple remote hardware. you may wish to close that application if you experience any problems using your remote in Hulu Desktop". The problem is that I have no idea what this third-party application might be.
Using Activity Monitor, I've systematically gone and deleted every process that is running (and that I think is non-essential). But this method didn't get me any closer to finding the culprit. Unless the culprit is my antivirus program (Sophos) because there are processes running from it which can't even be forcequitted.
here is what I have starting up when I login:
Quicksilver
GrowlHelperApp
iTunesHelper
AppTrap
GrowlMenu
Xmarks for safari
Dropbox
SophosUIServer
here are the (3rd party) applications I've installed that I'm pretty sure make use of the apple remote
Boxee
Hulu Desktop
Miro
PandoraBoy
Plex
The last thing I want to do is Reinstall the OS from scratch (getting all of my work related software, photos, music, etc back to normal would take hours of time that I just don't have). Any suggestions about what I could try next would be GREATLY appreciated.

I've found the problem.
These applications (boxee and plex specifically) are configured to hijack the apple remote to make the menu button open them instead of frontrow. So the problem I had was 2 fold.
First: The applications were competing with each other for control of the remote. Since I had them both installed, and they were both configured to keep tabs on what the remote was doing, they were both competing for the remote IR and it was causing problems. Deleting Plex fixed this issue, but I could have just as easily reconfigured the settings on both of these applications to ignore the remote IR when the applications were not running (which is what I have now done with Boxee).
Second: Both applications were running on an older version of the Remote IR (which was updated when snow leopard came out). So in their attempt to hijack the menu button on the remote using the old driver software, they were locking the whole thing up. To fix this problem, I downloaded a program called candelair which allows software to interact with the remote using a kind of legacy compatibility mode.
Now, the remote behaves normally when Boxee isn't running (so I can use it to manipulate itunes, Hulu Desktop, and MS Powerpoint with no problems). And when I've got Boxee running, it works with that just fine.
Here's hoping that this solution helps other people out in the future.

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