I'm using WinAmp 5.08e and have not had any problems with the audio quality. I also use the DFX plugin to enhance the sound.

Used to be a 2.9 user along with the MExp plugin (playlist manager). But version 5 has it's own playlist manager and it works well. I switched to version 5 because version 2.9 would not work with WindowBlinds that I had recently installed.

Glad I made the switch.

Maybe your system is low in resources and WinAmp 5 might require more resources, thus pushing your system and causing sound issues??