the really frustrating part about the transform matrice problem is that a ship will say it is -90 rotated when imported but not be actually visually rotated until you freeze all transforms. But what's even more frustrating is that if the model is transformed before importing without being reset and then rotated in XSI it will be rotated even if you think it looks good in XSI and freez transforms. I spent a few days trying to figure out why a ship that was imported, looking fine in XSI and had freeze transforms was still pointing straight down. It was because XSI freezes its transforms, but doesn't cascade them down to the model, the coordinates get rotated on export (found this out by exporting the XSI and then reimporting the XSI into the same scene, the nulls came in properly and the mesh was pointing the wrong way!) so if you are working just in XSI you just need to freeze transforms, if you are importing from another format you need to make sure the same thing is done before it exports.
I am working on a max tutorial, but it takes time to make these things and I am more interested in getting my ships in