Are you triggering them correctly in-game? They're stored with every other sound file in the GCFs, so unless EVERYTHING is broken or you've got some incredibly obscure MP3 glitch, there's something wrong in the map itself.
Trust me, they're .mp3 files. If you put 'wav' on the end, they'll break. It should be linking to 'music\hl1_song21.mp3' for example. They will NOT work in the sound browser. They WILL work in game if treated as a normal WAV.
Oh, and for the record, I use MP3s, and they work fine.