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Ok this has been going on for a little while now. I go on Halo 2 and have like 12 friends online. I get bored and go on bungie.net and it says no ones online but i know my friends are!!! Save me eskimoe pie your my only hope. Or maybe bungie'll help? I dunno
Give it time and your friends list will appear correctly. If it does not after a week, week and a half or so, try contacting Achronos about it.
I believe this is more a problem with xbox live. My contacts haven't been coming up in MSN consistently either. I believe they are aware of this problem and currently working on it. Go check out the xbox.com support forum.