If true then they are likely booking you into an award booking class if upgraded, meaning no miles credited anywhere. This also happens to CM flights upgraded with a UA RPU, it books into CM's award class and I had to fight tooth and nail to get UA to credit it properly as the original booking class. If that's the case, you'd be unlikely to have the same luck with MS since you're using a 3rd party company to do the upgrade rather than an instrument of your FFP.