Different bitstream produced by Quartus II v10.1 - Windows Linux

You should check that your timing constraints are correct. First check the frequency of your clock sources and generated clocks (you can use the report clocks function in Timequest and compare the frequencies with the real ones).

Then check that all your false paths are real false paths, to be sure that Timequest doesn't forget to analyse some paths.

Then check that all your I/O pins are constrained (there is a report for unconstrained ports), and that their constraints are correct.