If you're using MJ8, there is the Media Editor program that is included. You can find the shortcut to it in your Start/Programs/Media Jukebox folder. You can convert the files by opening them in Media Editor and then choosing Tools/Format Converter. The parameters should be set to
Sample Rate: 44100
Bit Depth: 16
Channels: 2
It doesn't look like Media Editor has a batch mode, so if you have a lot of files, this could be a little tedious, as you have to do them one at a time. You could do a Google search for a free audio editor called Audacity. I've seen it recommended quite a bit at Hydrogen Audio forums. I don't know whether or not it has a batch mode, though.
Also, before you convert them all, I would do a few of different durations and see if they are recognized by your burning software. I use Feurio, and it won't let me burn a track shorter than 4 seconds. So, there might also be an issue if the duration of the clips is to short, ie., less than 4 seconds.
Rob
Also, when I say convert, I'm not talking about converting the wav files to another format (like APE, or MP3), I'm talking about converting them to higher resolution wav files. So, your going to put a wav file in and get a wav file out.