The one case that I know can cause this would be a brush entity that isn't tied to any of the geometry in the map.
An example of this would be blackeagle's prison map before he completely remade it: the compile log had no errors and the vmf loaded fine in hammer, but the map instantly and seemingly inexplicably crashed CS:S the moment it was loaded. Eventually we discovered that he had a func_physbox entity that wasn't tied to any brush - it was registered as an entity in the vmf but there was no geometry that was using it so it caused crashes because the source engine probably couldn't read it.
When you deleted everything in the map to check if the vmf works, did you delete everything in the entity report? (in the top bar with 'file' and 'edit' map>entity report) If not then this is probably the reason why.