In our case not.
We have a Asus Sabertooth P67 (pci 2.0) and a Gigabyte GTX 960 (pci 3.0) black screen on monitor en red VGA_LED on mainboard.
So it is not always compatible.
We have latest firmware in P67 and bios default loaded.
The card is bad or not properly installed. Most often the problem is power or not fully seated. But they are fully compatible.