Hi Kendras,
when you get time, if you select any 3d model chunk in s3d, there is an uncaptioned parameter to the right of the "Model info" section, about under the Import/Export buttons, whose exact meaning is beyond my understanding.
In most SHIII files I have seen so far (and for all the 3d objects linked to a material with SpecularMask action controller and with an alpha channel in their texture), the said parameter is set to 4, but in our files it is set to 6.
I start wondering if this is not the culprit for the corrupted reflections on our model. I know the chance of this being true is low, but as someone else said: "when you have eliminated the impossible, whatever remains, however improbable, must be the truth". Maybe worth a try?