I just tried this as an an experiment, and I'm getting the same result. That is, I put the Vocal Transformer effect on a single track in a multi-track project, export the Master Mix as an mp3, and I'm getting silence, too.
It's an extra step, but a workaround is to export as an aif or wave file first, then do the conversion to mp3.
If you do that, make sure to set your submix to the same number of channels as your track (i.e., stereo or mono), so that the resulting file you export is the same channel count, instead of surround.
Hope that helps!
EDIT: BTW, I submitted this as a bug to Apple.