I know this has been mentioned in the past but I would like to bring up something that I think may be relevant.
There are certain sections of the maps that I know from flying around in no clip, have really tall collision boxes. I believe that one of the reasons for the invisibility is very fast changes in height (not that I think its the only reason). Something like the same reason sometimes you shoot someone and they fly into the sky or players stutter up and down when moving up and down ramps.