1) The file is bad. There is something corrupt in the file. Re-rip the file from its original CD again to fix the problem.
2) This is a known bug in Beta 11. Download and install the Hijack kernel (link at the top of this page) to fix the bug temporarily until the next software release.
3) Different decoders will behave differently (unpredictably) on bad files. If Winamp plays silence on the bad frames, that's just a feature of its decoder. It's not "muting" anything, it's just choosing not to decode the bad frames.
If you wish to check a file for bad frames, use MP3Trim.