while researching blender to .x, i came across info on colllada to unity. do a google, its out there. don't have a link, since i'm using .x, not .DAE.
i did discover about a dozen idiosyncrasies getting blender to export.
some probably apply to exporting to unity.
the issues are detailed in the comments of the skinned mesh code i recently posted to my gamedev info journal.
they include things like exporting multiple animations, etc.
i think the blender export info is at the end of part 2 - maybe part 3.
might provide a clue as to whats not set correctly for export.