timing simulation with modelsim-altera

Sorry I cant help here - I never run gate level sims (RTL simulations and timing analysis are all you need 99.99% of the time - 10+ years in industry, never needed a gate level sim).

Why are you trying a gate level simulation? if you are relying on gate delays for timing, then you are going to run into problems. Gate level sims will only show the worst case, and in reality the timing will vary.