It is not an issue with my profile because I can use it with Map->Tools->Export->Shape. It seems like when I try to run the command the selections are lost and I'm not sure why.
I also get a problem when I try to select polygons and then go to Map->Tools->Export->Shape where they are lost there as well. However, if I select them again, import the same profile I am trying to use above and run it, it exports to a shape file correctly.
I have AutoCAD Map3D 2011 set to allow selections before command and it works for other commands