TF2 stutters with high FPS, low ping

It would be a good idea to look into the Catalyst Control Centre for graphical settings. You can use the CCC to override (or even compound) graphical settings for games, and this may be the case for you. You should try finding the settings for anti aliasing, anisotropic filtering and texture quality settings (to start). Try turning those down, and they should directly help you out.

Failing that try uninstalling your graphics card drivers, rebooting, then installing new graphics card drivers from amd.com .

What it sounds like is that your graphics card is applying texture improvement processes to the smoke textures, processes such as anisotropic filtering, and it's simply set way too high.

Have you been using many mods? Some are known to leave garbage data in saves that slows the game down after the mod has been updated or removed. Try starting a new game with 0 mods and see if the slowdowns continue.

Also, make sure your mods are compatible with the version you're running.