This is a known limitation of the architecture: the browser will clean up the Javascript context when the user navigates away from the page, which destroys the Jabber plugin instance.
Workarounds can attempt to maintain the page/Javascript context as long as possible: using iFrames or Ajax to update the UI without navigating, launching a popup window for the Jabber telephony UI, etc. Some developers have successfully managed the Jabber code and plugin in a Chrome extension, which stays active for the lifetime of the browser.