Microsoft needs to coordinate Windows accounts and Office 365 accounts better. More than once I ran into problems related to the distinction between my Windows account and my Office 365 account. Windows accounts, formerly known as Live (and Passport before that), are a distinct identity system from that used for Office 365.
Some of my migration problems were due to the unusual situation I apparently presented: My Windows ID was the same personal email address that I was using on the Office 365 domain. This confusion caused a 24-hour delay in getting the Office 365 domain properly set up and I was only able to do that with help from Microsoft support. I had to cancel my Windows ID and create a new one and even then, I had the impression that the system is unequipped for this circumstance and that the operations people had to do some sort of manual override.
There are many other circumstances where you'd think you could use your Office 365 ID instead of your Windows ID: Logging into a Windows 8 system or Windows Phone (pictured), for example. But unless the Windows system is on a managed domain, you'll need to use a Windows ID to log in and then log in separately to Office 365. This isn't a major pain, but it feels wrong and some users undoubtedly will experience the same confusion I did.