Is it the one to the far left or far right (fan side up, laying flat)? Reason I ask, there was a post (which I can't find) in a early 980 thread. Some guy with a 144 Hz monitor was only getting 60 Hz while using DP. Some user pointed out, might be Veteran not sure, to use the Primary DisplayPort, which fixed the problem. Can't remember what he said but it was either the far left or far right one.
On the graphics card side of things a DP is a DP, there's no bandwidth and thus connection difference on the 980 connectors. But there are two scenarios that come to mind: You could/would assign a primary DP is in the BIOS, so you could boot on the Primary DP opposed to preferring say the HDMI which now would be the secondary display. So that could be labeled as primary DP. And if a graphics card has a multi displayport group running over a secondary BIOS, it could force 60 Hz to keep enough bandwidth for the multi-display group. One 980 card that can actually do do that is the Gigabyte 980. With that card the DP directly above the HDMI connector would be linked to DP port group 1 and 'could' be named a Primary Display Port connector.
one thing I've noticed is that by default the 1080p resolution is selected which doesn't have higher refresh rate while it does if you choose the one under PC