It might be worth the time to convert ALL the files to mp3 or OGG. If you have the space, even to FLAC (lossless)
You can obtain winff from Synaptic. Then
winff>Add> (select all>open)>convert. In the output tab, Convert To>Audio and Preset Device> mp3, OGG or FLAC.
Like I say, bit of time and effort. This way, you will have all your files in one format, easily recognized by both Amarok and Rhythmbox. You could then burn them back to CD's. Be aware, unless you're dubbing from a lossless format, copies of copies are degenerative.