Once more (see post #2)...
All other conditions remaining the same, and no limiting factors involved, reducing thrust will increase the time required to accelerate. Since rotation rate is assumed to be constant regardless of thrust setting, a higher Vr will be required to reach V2 at the same point in the rotation/initial climb.
If you tell the FMC you are using full TO thrust, but you tell the performance computer (or it tells you) to use TO2, the Vr values will likely be different. Once the parameters are consistent in the performance computer and the FMC, the displayed speeds should match