PCI+Nios problem with Cyclone III device

Hi,

I think I have posted this question in a not related section. I will repeat it here in more detail:

I am designing a peripheral card which interfaces PCI bus. My board is using a Cyclone III chip (EP3C25Q240C8) which is configured to hold a simple system consisting the PCI compiler core from Altera and a Nios II processor.

When I configure the chip - before the host PC is restarted and the card's driver is installed - I can run a simple "Hello World" application on the Nios without any problem. As soon as the card is detected by the host PC, the Nios II IDE fails to program/run the application on the processor.

I have tested the PCI card from the host PC by reading/writing to it's address space and it seems that the PCI core is working.

I have accidentaly decresed the VCCIO of the Cyclone III IO banks from 3.0v to a value around 2.65v and strangely Nios started working (at least with my simple hello world program). But, I know there is something wrong with this!

Any idea what may have caused the problem?

Thanks.