Are you using any third-party plugins and/or profiles? VAICOM PRO perhaps?
If so, you'll want to ask the author of that product about this.
VoiceAttack by itself does not alter input settings unless explicitly set up to do so (the exception being microphone volume being set when the speech recognition engine starts, which is done by the speech recognition engine rather than VoiceAttack itself, and should only occur when the engine is initially started shortly after VoiceAttack is).