You can only be signed into messenger on one computer/(console) at a time. So when you sign in via the xbox you are signed out on your computer. The only way to stop this would be to disable log in on your 360.
It also works the same if you use messenger at home and work.
Sign in to Xbox LIVE, go to the Xbox LIVE blade, then select your gamercard and press A. Go down to 'Auto Sign-in' and press A. You can set your preference for Xbox Live and Windows Live Messenger separately here.
Thanks, elmafia. You're the first person to actually give us the step-by-step directions. Everyone else is saying "Oh, just look on the dashboard somewhere. There's an option to turn it off there." ...Of -course- there's an option to turn it off, I was just too lazy to figure it out. :)
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