Calibre 2.7 introduced a new way of dealing with Jobs that have end-of-job dialogues. Rather than popping a modal dialogue box that takes control, a notification message is shown (bottom right where the Jobs spinner is) that does not require an immediate response.
See this thread for background
Downloading metadata in background
The Count Pages, Modify and Extract ISBN PI's have automagically inherited this new job complete notification scheme... except when Extract ISBN fails to find an ISBN, then I get the 'old style' modal popup dialogue
BR