if that doesn't help you can in edit mode select all (key A) then pick "recalculate" in toolbox or press (Ctrl+N)

Thanks Artfunkel! Hope that Valve will accept recommendation for you as service provider. You certainly deserve it.

@Artfunkel: Is there possibility to change default spheres in SMD tools (in script) to something like this: https://www.dropbox.com/s/ixl1kxpwcjual9v/Screenshot%202014-02-24%2018.16.12.png ? I know I can do it manually for each bone, but think it will be more helpful than spheres and it would show orientation of bones.