Hmmm. Okay. At this point, it should have done something, and it should not have made it invisible.
To clarify, these .sdr files went in to the Freespace2\MediaVPs\Data\Effects, not Freespace2\Data\Effects, right?
Because if the regular mediavp shaders that are in 3.6.10 work for lighting (with the exception of weapons effects on ENV), then so to should the original Unified Shader package. There should be no invisibility or "black" ships with either of them save in the second set and only if/when -normal is turned off.
On the upshot, all this tinkering made me discover that the -height option broke the unified shaders, so I was able to correct that, at least.
The down side is, I'm now even more confused as to why nothing is working the way that it should. Some folks have suggested that it's because you are using Omega drivers, but I'm dis-inclined to believe that, having used them myself. But it is about the only option left that I can think of as part of the troubleshooting would be to use the same version ATI drivers that the Omega drivers you are using are based on.
It's entirely up to you on that one though because I know driver swapping is not always fun, and I've never seen deficits from running Omega drivers.