I just noticed something else, I installed CS:S beta, which is a separate install and has separate achievements and for the beta the achievements are counting correctly, but on my profile page they both show as Counter-Strike: Source. They show up separately, but it doesn't indicate beta in the name on here.
So I fired up CS:S a couple nights ago for the first time since they added achievements and I was popping achievements all night. Checked my GB profile page the next day and it said I unlocked 40 counterstrike achievements. I knew I got quite a few, but that seemed kind of high to me so I counted and I actually only had 20, exactly half. Played again the next night and the next day my GB profile page said I unlocked 12, I counted them again and I had only gotten 6 the night before, again exactly half.
Not that I'm complaining about all the achievements, but something's bugged there.