After CALEA was extended to online services in 2006, Skype was legally required to implement wiretapping. They didn't, and stated they had no intention of complying with CALEA publicly, but never seemed to have been targeted by the DOJ over their non-compliance.
But they were still legally required to have done so, and the DOJ could have sent them up shit creek if doing so ever became a priority.
What's changed now? Probably just that Microsoft's legal division wasn't comfortable having that kind of regulatory non-compliance under their watch. Microsoft gets a lot of scrutiny from the DOJ and probably aren't particularly keen on being hauled up on new charges over this issue.