@MenDax: the problem is that some HL singleplayer maps contain a reference to '\quiver\valve\sample.wad'. So when r_wadtextures is enabled, HL will crash because there is no sample.wad file. Fortunately that's easy to solve: just copy another wad file (or create an empty one, it doesn't matter) and rename it to 'sample.wad'.
A while ago I ran into the same issues as you did, but thanks to livewired's mention of r_wadtextures (thanks!) and an empty sample.wad file, I can finally finish that 'Half-Life: the Dithering' texture mod:
@23-down: sorry for nitpicking, but... it's 256 colors, not 256-bit, and textures sizes must be multiples of 16 (due to mipmaps). .jpg is indeed a poor format for textures, but what's so special about .tga? And what does that have to do with map compile tools?