Hi, there.
What VoiceAttack does is it gets a handle on a window and then starts sending input to that window. There are two ways to do this. You can either you choose, 'Active Window' or you can specify a window. When, 'Active Window' is selected, whatever window that is in the foreground and focused will receive the input sent by VoiceAttack. Specifying a window will make VoiceAttack seek out that window, bring it to the foreground and focus it before sending it input.
In your case it sounds like you probably have Active Window selected. It's highly likely that something is in the foreground that may not be what you are thinking it is. Would you happen to have Synergy or TeamViewer running by chance?