The only bias is in the initial default MFU list, the one that appears upon a fresh login. In Windows XP, the default Start menu MFU contains six slots. The first three point to Windows applications, and the second three point to programs chosen by the OEM. (If the OEM chooses not to take advantage of this feature, or if this is a boxed version of the product, then the second three slots also point to Windows applications.) Which specific three (or six) programs get displayed depend on the system configuration, so it's not like there's a single initial Start menu that applies to everyone.
Once those initial MFU items are selected, the Start menu algorithm proceeds in a vendor-blind manner. (Indeed, it doesn't even know who the vendor is; no part of the algorithm looks at file version information.)
The precise algorithm that is used for determining which programs go on the MFU over time has been reviewed by government-appointed regulators, who have not raised any concerns over vendor bias.
So I hate to say it, Chrissy, but I think it's all in your head.