Well, atleast it will have problems showing them with 'show non-shader images' unchecked
And I wouldn't check this because it'll end up with lots of original textures showing up, which weren't ment to be used
Another reason could be the format of your images: jpeg must be rgb, tga files must be 24 or 32bit files.
I have the same problem...while loading my map it says textures/base/virus FAILED! But in the 3D view they are showing up nicely. When I select the textureset BASE (my custom set) they also show up nicely in the textures window. But after compiling during gametest, the textures are replaced by the first texture in my custom set. I use 32bit tga files.
Use 24-bits tga (or jpg) for images without an alpha channel, 32-bits for textures containing an alpha channel. Only use an alpha channel if you need transparent parts, it's a waste of memory otherwise.
If you use spearhead, try to copy the folder contents from main into mainta or vice versa, start MOHAA for testing instead of Spearhead or - best - forget about Spearhead at all.