It has to do with both the tangents, and how the polys join with other sections. I just havent figured out how to fix it in XSI yet.
In fact, it have do to with normal...
I cannot help you with XSI since XSI hate me... but it will surprise me if XSI don't have a function for correct it...
By example, with blender, there is an option to flip all faces to define outside/inside. In EDIT mode, Mesh->Normals->Recalculate Outside... that flips allnormals to face out. That way you don't have to flip them one by one.
The only way that i can MAYBE help you is to have the model in .obj and in .mesh ( text mode )...
By the way, the ConvertXSI.exe is not fully bug free... by example, there is a problem with U1V1 value when tangent are set on "False"... this lead to shadow jumping from one poly to a other ingame... this can be corrected with notepad for softer shadow...
As how it look in other software, remember that a lot of these software are complex and can correct themself some minor error... like you wrote, the sins engine is not so much forgiven... in fact, some modeling method who will work in other 3D software are fully incompatible with the game engine...
EDIT : no sure that it will help you but take a look at http://isiforums.net/f/showthread.php/193-Modeling-How-to-solve-the-Flipped-faces-issue ... i think that it is related to your 2 problems ( flipped face and shinny poly )