I have 83 out of 99 achievements in the Orange Box simply because I cannot get the Team Fortress 2 achievements to pop. I don't know what the problem is, but I will link you guys to the file I used and the website. Here is the link, just scroll down a bit and you will see it. http://gamecheats.xploder.net/showthread.php/66930-Load-and-Pop-List-Saves-Included
As far as I remember people have had this problem before, your best bet is to play Team Fortress 2 or use an achievement unlocker. Sorry that it doesn't solve your problem.
Sorry, I'm not going to mod my achievements, I don't know if you know this, but you can get reset for modding achievements.