Hmm...
I can't help with any Linux insides, but I can tell you that this is the exact same error Win9x Users get.
There is one Win2k OpenGL ICD (the latest one existing), which does support S3TC, but it just runs into another error
I wonder if there is any other Texture Compression one could set in the config File of UT2003 ?
I've also read that it is possible to run with the Textures uncompressed, some form of that was included as a workaround for 3dfx cards for UT2003.
But getting this one solved will be a tough one.
I can only highly recommend to register at the ina Forums of Epic, and maybe Post your request right there, where (at least sometimes) Epic Officials scan the Postings and indeed take points out of them to realize or work on.
At least in the Windows World, they said OpenGL was completely unsupported, however... Although for Linux, there is no real alternative to OpenGL, so they must provide
some kind of support for it.