Functional Simulation is Correct,But Timing is Incorrect

It is rather difficult to say where you have gone from the very limited information you have posted.

Yet here are some guidelines

1. Timing simulation is wrong means some part of your code with clock tick events has a mismatch somewhere.

It is a good practice to start with reset and intialize everything

2. Your .vwf should give you an idea where it is going wrong. Stretch your time bar to get a clear idea of waveforms.Comparing the .vwf files of functional and timing simulation might give an idea.

3. In timing simulation, for the first clock cycle data may not change.

4. If you have written lot of loops within a process ,it will be a good idea to check it.

5.check the warnings given by QUARTUSII. If you find anything suspicious ,then right click and get the help for it