Okay, NOW I think I see what's going on.
Atherton25, please look in your FFF settings, do you have "Search by Title/Author(s) for If Story Already Exists?" on or off?
If you have it off, please check it on and try your test again.
What I'm seeing is that the identifier search is 'honoring' Virtual Library and the title/author search doesn't. And because I always have "Search by Title/Author" on (it's on by default), I--and most users--never saw this.
Code:
## honors VL??
self.gui.current_db.search_getting_ids('identifiers:"~ur(i|l):~^%s$"'%re.sub(r'https?\\\:','https?(\:|\|)',re.escape(url)),None)
## ignores VL??
mi = MetaInformation(book['title'],book['author'])
identicalbooks = self.gui.current_db.find_identical_books(mi)
I'm going to go look in the Calibre code at these methods to see what's different between them.