Im using Universal Web Adapter (Chrome). I have never experienced this on IE only in Chrome. Does BrowserStopMethod in Web Adapter Properties have something to do with this? Mine is currently set in "StopTrackedDocuments"
The universal web adapter is actually connected to all instances of Chrome once the extension is loaded. The best way to get the behavior you expect is to make use of the AcceptedDomains property of the adapter. If you had an adapter for Pega.com and set the accepted domains to include "pega", then only those pages open in that domain will close when you stop the adapter.