Hmmm... can you please give us some more system specs/info
, eg. soundcard & drivers, DirectX version (should be 9.0c), dxdiag log, my_plugin_list, what filetypes you're playing (eg. are they all just .mp3), etc.
The same thing happened to me a week or so ago, where I left Winamp playing some ambient music all night, and when I woke up all I could hear was the same second or so looping over and over. And like you said, Winamp was still functional, and I could play other songs etc, but the looped sound was still playing in the background, even after closing winamp, and the only way to get rid of it was to kill the winamp.exe process in Task Manager (the fact that the winamp.exe process was still there suggests a problem).
Note, I've also got one or two extra 3rd-party plugins installed, but no dsp/effects plugins are enabled.
As a test, can you try switching to WaveOut Output (Prefs > Plugins > Output) instead of DirectSound Output, and let us know if the problem still occurs (note, DirectSound Output is recommended under Win2k/XP, not waveOut, so this is mainly just for testing purposes).
In the meantime, I'm moving this to Bug Reports, until the issue is either reproduced or resolved ...