I had the same problem as the original poster- startup hanging at "Loading protos (clearing old...)" for over an hour. I had tried a protos.tab mod (changed Meleny's hair to blonde) to get my feet wet using Phalzyr's Proto Ed. I see after searching that World Builder is preferred, but I may get the same problem. Ir I revert to the original protos.dat, the game works fine again. So a quick question- does the module need to be activated again from the front end after a protos.tab edit?