I had one installed - Marco's Advanced editor/quick reply - that I thought may have been the reason the popups started but it was installed months ago. Completely uninstalled and removed it but this did not stop the leave page messages.
I found a temp solution to stop the leave page message in jira by doing this:
edit clientscript/vbulletin_textedit.js file
change it this:
{YAHOO.util.Event.addListener(window,"beforeunload ",this.exit_prompt,this,true)} to:
{YAHOO.util.Event.addListener(window,"beforeunload ",this.exit_prompt,this,false) }
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