I was working with Blender for the last few months and it can be quite confusing. Yesterday I had this weird occurrence where I had call bpy.ops.object.select_all(action='DESELECT') everytime before changing the matrix_world.translation values of some meshes. (Even though I didn't select anything in between). It took me hours to find out why the meshes weren't moving correctly.
I guess Blender is not perfect for using it with python only.
I guess Blender is not perfect for using it with python only.