Heyaz,
I know there are some work arounds but this works for auto import of maya files into Unity. Ive only done this/tested with Unity iPhone.
in FBXMayaMain.mel add this at the end:
if (getApplicationVersionAsFloat() >= 2009.0)
{
loadPlugin "!//MAYA_PATH//!/Contents/MacOS/plug-ins/fbxmaya.bundle";
eval ("source \"!//UNITY_TEMP//!/FBXMayaExport.mel\"");
}
in FBXMayaExport.mel add this before the line line about FBXExportShowUI:
if (`exists FBXExportFileVersion`)
{
FBXExportFileVersion FBX200611;
}
Thatll get ya running with auto import chocolaty goodness. It will no longer crash maya to import if your using maya 2009.