Blender STL files not working in Makerbot program?

I created a stand for a tablet in Blender and saved it as an STL file. When I open the file in the Makerbot program the preview for scaling and rotating looks exactly as I had it, but in the print preview before I begin looks nothing like what I had, putting filament in blank spaces and sometimes deleting whole sections. It does this for all my STL files, not just this one. I have tried everything I can think of, but nothing has worked. Has anyone else had this issue, and does anyone know who someone might fix it.