VoiceAttack uses standard Windows API methods to perform virtual keypresses. These should work just like your physical keyboard does, in the majority of applications.
That also means that normal output produces lowercase characters, as long as Shift isn't pressed down, and Caps Lock is off.
If you're using the "Quick Input" action, VoiceAttack will press the Shift key for you if needed to produce the character you've entered using the keyboard layout configured on the "General" tab of the VoiceAttack options window, however it will not release the Shift key if it's already pressed (nor will it turn off Caps Lock; if that's on, the case of the input will be inverted).
I.E. make sure Shift isn't pressed, that Caps Lock is off, and if you're using the "Quick Input" action make sure the contents of that action's "Text" field are lowercase (or the case you want them to be in)