I guess if they are protected, Winamp doesn't send them through Stereo Tool (otherwise any plugin could just write the raw audio data to disk, thus bypassing any protections).
So there's probably no easy way to solve this.
If you REALLY want to pass the sound through Stereo Tool, there is one possible solution (depending on how well the protection is implemented): Send the output from Winamp to the stand alone version of Stereo Tool. You'll probably need the program Virtual Audio Cable to do this (unless you have an ESI sound card - the driver of that card supports sending data from one application to another). I don't know if it's worth the trouble (probably depends on the number of songs that you have issues with) - if you want me to give more details about this solution let me know...
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