Makerware automatically position objects I suppose.
Maybe try to position in Netfabb it first to the right position, and repair it maybe.
First set the used platform size under settings.
The move the object by right clicking on the model // move // to origin // move. The point 0.0.0 is the center of your build plate normally with Makerbot. In netfab the 0.0.0 is at default left under. So you can center your object further by moving it's center obove the 0.0.0 point of Netfabb.
Do that while looking from the top.
Export that stl, and see if it shows up.




Bart