3,3v pci ciclone iv

Hi

I am working in a PCI proyect. I developed my pci core in a CPLD (EPM1270) that it has pins 3´3V PCI compatible, so I dont have problems with this device and it works fine. (I dont use transceiver 3,3V-5V)

Now, I´ll migrate my proyect to a FPGA CICLONE IV (EP4C6) but while I was working in a new documentation I saw that the device has pins 3V compatible

Why one of them is 3V PCI and other is 3,3V PCI?

Can I have problems with this?

Regards

Javi