same problem, new case, new solution?
I have recently split my first map into 3 pieces so i can make them longer, better, and more detailed. the initial map (killing_glados) had an error a while ago where it wouldn't load the map in the game, just crash on startup, which i managed to fix by deleting a box. 
now, the first piece of my now split map is not working, and crashing the game after it is loaded. i'v already tried deleting my newly added box.
(the map is a WIP and so it looks really weird right now.)
I've also tried deleting the unfinished catacombs and the instance, but no luck. 
Aperture Science: We do our science asbestos we can!
Only thing I can suggest is to try and isolate the problem.
Hide all entities first. (then you will know it is an entity if it crashes then).
Hide all triggers and un-hide everything else etc. etc.
ah... good solution. well, I've already isolated the whole underground catacombs and the instance, so i know it isn't that. now, i'll just search around in the brushes/entities, whichever seems to hold the problematic object.
Aperture Science: We do our science asbestos we can!
Ok, now this is really no making sense. every entity has been removed, it still crashes. every brush has been removed, still no luck.
Aperture Science: We do our science asbestos we can!
sometimes the vmf is corrupted. just copy everything and paste it in an empty, new map and save it. Maybe that works 
already tried that too. i could only play it after i deleted everything and restarted from scratch, so this may take some time tommorow.
Aperture Science: We do our science asbestos we can!