If you've ever done a fresh install of Win2k3, then the service packs, then installed IIS, then installed WSS 3.0, then fired up Central Admin, get barraged by security challenges and finally end up pretty much with a worthless Central Admin...

Try re-applying the service packs, especially if you installed IIS from media that pre-dated the service packs you just installed. I don't know what the exact problem is, but the symptoms probably aren't limited to WSS. One of the files that will fail to authenticate is WebResources.axd, which can be utilized by any ASP.Net application.

I can imagine a few people have run into this but I only found one page which described the symptoms and solution.