Me and my friend travelled back to Sweden from a one week stay in Turkey recently. My friend is a Japanese citizen but holds a permanent residence permit in Sweden. At the check-in counter, the guy asked if my friend had a visa and the permanent residence permit that's attached to a page in the rather new Japanese passport was pointed out to him. This seems to have caused a lot of confusion. First the check-in guy asked his colleague next to him to have a look at the passport. Apparantly this person couldn't decide what to do either so they called their supervisor who came and after studying the passport and the residence permit for a while, asked if it was ok for them to make a photo-copy of the passport and residence permit which, of course, was ok with my friend (never a good idea to argue with border security, we figured). We followed the supervisor behind the check-in counter back to their office where we were asked to wait. After a while the supervisor came back with the passport and the photo-copies. We where brought to what I can only guess was the supervisor's boss who again studied the passport and the photo-copy for awhile and then returned the passport to us and we were allowed to check-in.
Later, when passing through the passport control after the security check, the officer inspecting this particular passport again seemed to take his time and scanned the passport in his machine several time and holding the page with the photo up to a light and scratch his beard. But after five minutes or so, my friend was allowed to pass through. For everyone else, nobody spent more than 10 seconds looking at their passports.
At one time we asked what the problem seemed to be and were told that it's "just procedure", which is what I guess they tell everyone no matter what the problem actually might be.
When we arrived in Sweden, everything went smoothly and this is also the first time my friend (who is a frequent traveller) had any kind of issue with passport control.
My question now is if anyone has had a similar experience when trying to leave a country or even better, if someone who maybe has some experience in airport and border control procedures could comment with some ideas to what the problem might have been. In what cases do the check-in people need to keep a photo-copy of a passport?