Hey. Here's something I'm wondering.

When you are transcoding these files from WMA to MP3, are you trying to do the new file at the exact same bit rate as the old file?

In other words, if you started with a 32kbps WMA file, are you trying to make a 32kbps MP3 file?

If so, there's your problem. Just bump the bit rate of the MP3s up when you're doing the transcoding: Go up to 96 or 128 or something, and that will help prevent a large amount of artifacting that's generated by the second re-encode.

It won't remove the artifacts that already existed on the source files, but at least you won't be adding too much in the way of additional artifacts as part of the re-encoding process.