I had a case where a page opened a pop-up window, and on that pop-up window the icon toolbar was disabled, so I couldn't click on the NoScript icon to whitelist JavaScript URLs embedded in that page. So I thought I could invoke the NoScript menu from the page's page context menu. Indeed, I found the NoScript menu item, but clicking it had no (apparent) effect.
Does setting one or more of those to true get you a NoScript icon in the popup?
(It's unlikely all of them would be needed. Which one(s) you need depends on how you have your toolbar customised.)
*Always* check the changelogs BEFORE updating that important software!
I have a local test page that generates that type of popup. If you show a screenshot of where exactly you've put the NoScript toolbar icon in a normal browser window, I could try to check it myself.
*Always* check the changelogs BEFORE updating that important software!
about:config > set dom.disable_window_open_feature.toolbar to true
Should be enough. Now you should see a >> button, click that and you should find the NoScript toolbar icon.
(NoScript's context menu item still didn't work for me.)
*Always* check the changelogs BEFORE updating that important software!