No it doesn't matter with 2 cards. Works perfectly in Windows. Just can't OC in Linux.
A couple of options:
a) try Ubuntu 17.04LTS - it has an updated kernel that may be better with your CPU and motherboard.
b) try Nvidia' newer drivers
sudo add-apt-repository ppa:graphics-drivers/ppa
sudo apt update.
Then go to additional drivers - an every Nvidia Ubuntu driver release up to the recent 384.59 will be available for install.
Sometimes, you'll need to click open Ubuntu Software and update X Server control panel for that driver.
Remember, after switching drivers and rebooting you will need to re-enter:
sudo nvidia-xconfig -a --cool-bits=28 --allow-empty-initial-configuration