Our tipster claims to have spoken to several developers working at Sigil and at another development company that has Microsoft as a publisher -- we'd say the meat of the tip is on the same level of credibility as someone saying that the Government is tapping your phone (yes, I made a political joke -- the first comment to judge my political affiliation wins my apathy!).
According to our tipster, Microsoft intended to make Vanguard a Vista-exclusive title and Sigil didn't like it. The fact that XP users wouldn't have been able to play the game (limiting the user base quite drastically) and Windows Vista's notoriously slippery release date being the obvious disadvantages of such a move on the part of Sigil. If true, the motivation for Microsoft would have been that the title would be the first MMO to take advantage of Live Anywhere, Microsoft's online games platform which blends Xbox 360, PC and mobile phone devices: more Vista sales = profit!
It's credible that Microsoft wanted to use Vanguard as the first MMO to work with Live Anywhere but that Sigil didn't want its game to be Microsoft's guinea pig and therefore bought the publishing rights. With Vista around the corner, Microsoft wants to provide as much incentive for gamers to upgrade and by making big name games playable exclusively on Vista it can gain that incentive. At the very least we get a kick out of discussing the vague PR explanations of the reasons behind leaving a game's publisher during the beta stage. It's impossible for us to believe that simple, meaningless "varying visions" caused this massive, late in the game move.
Update 1: Brad McQuaid (Sigil CEO, creator of MMORPG Everquest) responds by saying "false rumor", but Joystiq commentator Jack Slater cleverly rebukes: "personally I would just deny everything if I was him, as there is no legal obligation for me to tell the truth on the forums but there is likely a legal obligation to keep the reason for leaving Microsoft undisclosed." Meanwhile, Ctrl+Alt+Del daydreams about how the meeting between McQuiad, Microsoft and Sony went. Funny stuff.