Problems probably related to signal propagation (timeQuest questions)

The timing will come from the design, and not fixable in timequest. Timequest can identify where the problems are.

If you post some code, maybe we can give you an idea of what the problems might be.

Another thing.. did you provide an sdc file? If you don't provide timing specs, it will default to try and achieve 1000mhz. This is very over constrained and can cause it to give up early. You might get a small improvement with realistic timing specs.