All I can personally say is that this happens on my machine as well.
Programmatical focus switching randomly breaks (not just for VoiceAttack, I have tried a number of API functions, with the "known" workarounds, in a standalone application, and it still won't work consistently or sometimes at all).
I have also had new windows spawned by applications not get a taskbar entry at all and only being visible in the Alt-Tab view (in addition to the actual window), and the taskbar not hiding automatically like it should until the start menu has been opened and closed.
At this point I'm just hoping the issue will fix itself with some random update, just as it likely broke in the first place.