I'm experiencing a similar issue, though my FPS sits around 40 without any lag in the menus, where the game seems to be stuttering frequently until I make some modification to the video settings, after which the framerate increases to 60. Any reconfiguration of settings does not return the problem until restarting the application (vsync, motion blur and anti-aliasing included).
System Information and Console output from both Steam and TF2.
https://gist.github.com/4583307
Nothing extracted yet.
Hello! I'm running Ubuntu 12.04 x64 w/nVidia Driver 310.14 and Steam x86, fully up to date. When I launch Team Fortress 2, the menus and game lag until I get in game, go to the video settings and change from MSAA 2x to 4x or vice versa. I'll be getting about 5-15 FPS until changing the setting and then I'll be at 60+ FPS. I'll be able to run well until, at some random point, the FPS goes down again. I've tried to see if I can force it by changing character or doing some action but it eludes me, it seems random. If I disconnect from the server, then reconnect... I will still be at 60+ FPS. However, if I change server then I'll always be at 5-15 FPS again until I change a video setting to get back to 60+. Steam Hardware Information and Console Output below.
https://gist.github.com/4582212
Edit: CPU and RAM usage during this time appear to be fine.