Thanks Tomek, I was on the right lines. I just needed to do this for all items in my repeater. I am opening and close the popup from c# code. Now it works. Hope this helps someone else:

protected void ClosePopovers()
{
   var autoRunScript = "$('.popover').popover('hide');";
   ScriptManager.RegisterStartupScript(Page, GetType(), "popoverclose", autoRunScript, true);
}

and then in my repeater

foreach (RepeaterItem item in RepeaterQuestions.Items)
{
   ClosePopovers(); ... etc.
}

Hi

If you want to hide all popovers, you must choose all elements which have popovers to show and then use .popover('hide') (e.g. $(".elements").popover("hide")). If you want more help please show me your code in snippet.

Regards

Tomek