If Nuance popup windows such as the "configure a foot pedal" box disappears without warning there might be a Windows setting causing this problem. This setting is located in the ease of access center in Windows 7 and Vista. To get to the ease of access center follow these instructions.
1. Click on the start button and in the search area type "ease of access" then select the ease of access center from the programs portion of the search results.
2. In the ease of access center un-check the option titled "activate a window by hovering over it with mouse".
This should resolve the issue.