Okay, this is another maya 2012ism that I am painfully aware of. I see you have layers, I do not see your outliner but I am assuming you also have groups or parent/child relationships?

It has been a while since I got maya into this mode but as I recall it had something to do with parent child coordinate systems. You'd click on a child objects component and the selection would appear at the parent+child coordinate location.


Do this as a test. Select all the objects in the scene and freeze transforms and delete history or ungroup/unparent everything. Then see if the odd behavior is resolved.