every normal bake i do thats part of the this mesh becomes screwed up. i tried different settings like global supersampler with or without it. I tried redoing the projection. I tried baking it in xnormals, which looks even more retarded. but if i rebuilt a mesh that is the same and bake the highpoly it is fine. My guess is…
if you reset x-forms and collapse down it does pretty much the same thing as the box trick (although a character artist was doing this to some hair last week and every time he reset x-forms the hair moved a bit...very weird :\ Box trick fixed it though)
I had this problem a while back. I just retouched it out in PS. Have you tried creating a box in the top view port, apllying a edit poly modifier and attaching your problem mesh to the box. Then delete the box in element subobject mode? you might have your geometery fliped and cant tell.