So, now I can really name the problem. It seems to be the tga skin of the player model that automatically makes the model transparent.
Just scripting if(d3d_transform==off){ent_morph,player,"a5version.mdl";}
does not work.
Maybe there should be a wait somewhere or the morphing should take place before the level loads.
The point is if I replace the model by a bmap-skinned one and update entities, all is fine.
Is there a way to switch off transparency with tga skinned models or do I need 2 versions of my player model?