Have you played back these files in both formats using another application?
I can see a difference in volume between the same sound as an MP3 versus a WAV file, even with media players like VLC.
Playing back a WAV file as a feature on/off sound is the loudest, playing that same WAV through the "Play a Sound" action is slightly less loud (on my machine), and playing that sound as an MP3 file, either through the "Play a Sound" action or an external media player, is quieter still (but again only slightly, on my machine)
Unless you have VoiceAttack installed to a hard drive rather than an SSD, there shouldn't be much of a practical difference, volume and storage size aside; especially for shorter sounds.