Marco,
just want to emphasize Clancy's point regarding the SDRAM clock phase. This phase seems to be very critical (at least at higher CPU clocks), and it depends on place & route.
In my specific design I had to ...
1) lock down the SDRAM-controller to a logic lock region close to SDRAM IO pins in order to freeze timing
2) adjust PLL parameters manually in the chip editor to values I was not able to get using the wizard.
Failing to do so resulted in arbitrary error patterns ranging from steady failure up to passing memory tests with data read/write but sporadic failures during code execution.
Rolf