Unity 4.1.5 crashing when building Win Standalone - Too Many GameObjects?

I've been designing a navigation system and it uses a lot of nodes. The current count is about 3,200 nodes for a level. Since the node count has been this high I have not been able to build the game (the game built fine when it had fewer nodes); the build screen pops up and the progress bar shows it gets to building scene 0 (the scene with the nodes) and then it crashes without error.

The editor log shows no errors, and the Unity bug reporter never pops up. Is there a limit to the number of GameObjects you can have in the scene? I'm using Unity Free btw.

I've tried using prefabs in the inspector instead of loading prefabs from the resources folder, I've tried building to other platforms, I've tried building a dev build, but nothing. The only way I've been able to get it to work is by deleting all the navigation gameObjects in scene 0, which obviously is not an option.