The current texture replacement code only works on the base map, so it ignores glow/spec/etc. I scrapped that old code and rewrote it from scratch to fix this problem. You can try out the new code by using one of my Xt-based builds in the recent builds forum. It's still 100% compatible with the old mission settings, but now it will replace ALL of the related textures rather than just the base map.
The only problem with the new code at the moment is that it won't work with scripting or SEXPs due to the design of the code (technically it can work, but it's a seriously convoluted process, so I need to rewrite it). That is the only holdup with the new code that is preventing it from getting into CVS. But, it will be completed and ready for 3.6.10.
Another feature of the new texture replacement code is a lower-level ships.tbl version. It has the exact same syntax as the mission version of texture replacement, but it sets the default textures, just like what is otherwise specified in the model itself. An example of how this is used can be found with the Fenris and Leviathan models in the MediaVPs. The POFs are essentially the same, except for the textures. So with the new code you can just set the Leviathan entry in ships.tbl to use the same POF as the Fenris, but still have a totally different set of textures. It won't save you a a ships.tbl entry, obviously, but it does save you from having to create extra POFs just to get different textures. And it also saves memory for everyone since they wouldn't need to have what is essentially two copies of the same model loaded.