Having this problem as well, might have some info that can help. I'm using pcsx2-v1.5.0-dev-1793-g52ec143-windows-x86 to show off the problem, but it also happens on 1.4.0 in OpenGL as well.
These are my settings, I have round sprites set to half in the HW Hacks.
My PC Specs:
Intel® Core i7-4770K CPU @ 3.50GHz
NVIDIA GeForce GTX 970
16 GB RAM DDR3
Microsoft Windows 10 (build 14393), 64-bit
It's actually difficult to see if not in motion because it's black vertical lines on the sides that fade in and out like an amorphous shape. But I think it might have to do with the way the game uses frame data. If you enable the Preload Frame Data HW Hack you get a static version of what the bug looks like:
Enabling the hack removes the sporadic nature of the issue, but then leaves it there permanently. I was able to reduce the size of the black bars by also enabling Half-Pixel Offset in the HW Hacks to make it look like this:
Significantly reduced, but adds that weird stuck line of pixels to the left.
The small black lines you can see on Direct3D11 might just be a smaller, less annoying version of the problem that occurs in OpenGL:
If anyone has any ideas on how fix it it'd be greatly appreciated.
EDIT: Setting Skipdraw to 2 forces the black lines to sit behind the one thin black line to the right, and almost completely hides the bottom black line. Closest I could get to removing them. Might try other Skipdraw settings later to find out if I push them off completely, but as is setting it to 2 is pretty optimal.