Speculation, so take it just as that.
As I recall, and this is from reading Road and Track many years ago, the V6 had bigger brakes than the Iron Duke.
At some time in the car's life, has the MC been replaced? If so, perhaps the MC was replaced with the unit from the 4 cylinder, and might not be delivering the correct amount of fluid. Again, speculation, but that might describe what's happening.
Just as a precaution, I'd also inspect the vac line to the booster - that's a long distance for vacuum to travel through a 21 year old piece of rubber. Check you vacuum at the manifold, and then at the booster, they should read the same.