Microsoft has a history of FUD and underhanded tactics against competitors. For example, remember the MSN/Opera thing? Microsoft tailored the MSN site to make it look like the Opera browser couldn't render the site correctly, making Opera users think maybe their browser was broken (reason to switch to IE). But then it was found that MSN detected the Opera browser and sent broken code to it by design. When Opera was configured to spoof the IE header (making MSN think that an IE browser was requesting a page), pages rendered perfectly.
Remember the Halloween document? Remember the memo from Bill Gates asking if they could make Windows 3.1 not work properly with DR. DOS and Microsoft did it? Microsoft is known for using underhanded tactics to make its competitors look bad, so between the options, Microsoft funding FUD reports is more likely than it just being innocent donations.