As of right now, for testing purposes the code is just doing a SendKeys("%^a"), then another call to handle the password (after verifying it is the active window). There is no need to make sure it is the active window initially because the purpose of the hot key is to pop-up a GUI window to type the password for toggling security. This initial GUI window is what I cannot get to happen. With previous program I was using (MagicFolders), I had no problem doing the same thing, but this one seems to handle hot keys differently.
My guess was that there is something inherently different at the bit level between SendKeys and someone physically typing the characters.