I had this problem way before using the Ninja. mesh. xml but did not really underthant what was going on at the time. The problem is that each time I load all my models at game start, it either creates weird blinding lights in the middle of the map or create a shadow that block the light, all depending on the model that is loaded (Ninja was shadow now fire golem from the web gimme weird lights)
I was not sure what could cause this problem until I made a test where I would load the scene before loading the model. It solves the problem… easy as that. Well, not that easy because in my game logic the model is supposed to be load before the map, but still, am now pretty sure it’s a bug coming from JME and not the models.
I had an similar problem a few days a go, I even create a post here ( dont know where it is now ).
In my case, I just figure out that depending on the node the object is attached, it gets different lights.
It happens because the object just get light from the lamps attached to the parent node of it.
Try to add all your objects into rootnode to see if there is any difference.
Also, when you import the object look at lamps attached in the scene, remove all the lamps.