Alessandro:
I am having the exact same problem. I have the the SOPC system, a PCI-X bridge, and several other components. I need to reset everything on a PCI reset, or reset the SOPC system and several components when I get a specific message from the PCI-X. I have tried making the reset as long as a second, or as short as less than one microsecond. The result is always the same--the NIOS II refuses to start afterwards.
The strange thing is: when I get a PCI reset (resetting everything) it works fine.
The NIOS II is booting from internal memory.
Let me know if you find a solution.