This often happens to me too. The missing surfaces have almost always been inside a group or a component, and often also had "hole-cutting" components placed on them.
It has almost every time helped to explode the model. The easiest way is to use the bomb.rb ruby script. After exploding, check that no faces have been flipped in the process, export to ATL but don't save the SU model!
If this fails, you might also try to use the 3DS format.
