How to keep Skype contacts merged?

I have configured Skype to display its contact list on the main People app, along with my phone contacts.

Some of them were automatically merged, for others I had to manually do it, but in the end every Skype contact was linked to its respective one on the phone.

(To better explain it, let's say that I have the contact details of two persons, Mr X and Miss Y, in both on my Google and Skype accounts. When I enabled Skype to display its contacts on the phone, the details of Mr X were automatically merged into a single contact linking the two accounts. But this not happened with Miss Y, that was displayed twice on the contact list, once for every account.)

Then I had to turn off the phone, and when I turned it on again all my work vanished: some Skype contacts were still merged, other were again splitted, so I had to manually merge them one more time.

Is there a way to keep contacts from various accounts united once I have merged them? And in the first place, what makes some of them to be automatically merged while others should be united manually?