Is it possible that you are saving in ASCII type? In that case it would be normal that your fbx get 3 times the size of the first one.
Also, take note that there`s a difference between the FBX exported from 3d apps, and the fbx saved in Mobu. The FBX exported is a sdk file format, and the one saved in Mobu is his native file format. In the fbx of Mobu, there`s a lot more info of stuff that cannot be understood by the FBX plugin.