I think the only agreement they have is the same agreement every developer has when they apply to submit titles to the Microsoft store. Making news from nothing? I found no Microsoft press release. But I didn't look too hard.
"We're thrilled that Amiga Games is bringing beloved classic game titles to Windows 8 and Windows Phone 8 starting this holiday season," said John Richards, senior director of Windows App Marketing for Microsoft Corp" is the only comment from Microsoft. Nothing about being please about entering into an agreement.