Schutze: US airways shuttle flights do qualify but please beaware the 5000 bonus miles may trip you up. To get the 5000 bonus miles you need to put in your US FF#. Make sure this will not impact your flights when you put in your LP number. If you do not put in your LP FF# you will have to go through extra work to get it posted --- such as sending in original boarding passes and ticket stubs.
My advice on LatinPass is keep everything pure. Do not try to earn FF miles on any other airline even if that segment is not requried for the LP bonus.