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I have checked over and over again the pin assignments and qsys settings ...
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The .qar file you sent generates warning messages about unconstrained clocks and paths and TimeQuest fails, so I think that is the root of your problem. Create an .SDC file for your project based on the example I provided.
This experience should help you understand that an HDL design consists of (at least);
1. The HDL design files.
2. The device constraints file (device type + pin assignments)
3. The timing constraints file (the .SDC file)
Cheers,
Dave