Adding to Rysc's comment about simulation runtime and what he said in his last sentence:
If you are doing timing simulation on a piece of the design to make the simulation run faster, then be aware that a compilation result on a piece of the design will probably have timing different from a compilation result on the entire design unless you are using the bottom-up incremental compilation flow to preserve the timing of the lower-level block. For that matter, every compilation result will probably have some timing differences because of variation inherent in how the Fitter works (related to the reason the Fitter has a setting called "Seed"). If the point is to check the timing, use static timing analysis (TimeQuest or the Classic Timing Analyzer).