It’s still connecting to both your Skype account and your Microsoft account. The only thing that Microsoft has really coalesced at this point is the program that you run. When you login this way, you’re actually creating two connections because you’re still logging into both services. For example, I can do video with a Skype account (which was its original use), but I can’t necessarily do video with a Microsoft account. All I can really do there is do normal IMing. In fact, the capabilities of each connection are ever so slightly different. I can log in with my Microsoft account, but several of my friends (who were in the same position) now appear twice: once with their Skype account and once with their Microsoft account. Skype suggested that I merge the two, so I did. I had a Skype account and a Microsoft account.
