The timing tools use a different methodology for setup and hold analysisthan the simulation tools. The timing tools use a combination of min and max numbers in order to perform worst case timing analysis. The simulation tools use either min or max numbers.
For example, for a setup analysis, the timing tools use max data and min clock delays in order to get worst case timing results. The simulation tools use max for both data and clock, or min for both data and clock.
This explains why you might see differences in the simulation and timing results. The timing tools are the sign-off tools, so your design should meet timing to guarantee performance.