Jammedstab, I think you're on the B744? I'm not 100% sure I've understood your question but I'll give it a try. Keep in mind that Vr must always be in excess of 1.05 VMCA, among other things.
V2 speeds on the 744 are essentially independent of thrust rating (as they are always well in excess of the minimum required 1.1 VMCA) and only depend on flap setting and weight, so the FMS precalculated V2 will usually immediately agree within one knot or so of the company computer-calculated V2 as long as the weights and flap settings coincide.
Vr however is more limited by its minimum of 1.05 VMCA, and as the default setting in the FMS is full takeoff thrust, the FMS precalculated Vr may initially be several knots higher than the company provided one (since VMCA at full TO will of course be significantly higher than VMCA at TO2). When you then input into the FMS the actual rating you will use, especially if it's TO2, its precalculated Vr should drop significantly and may then closely match the company provided one.