Affecting Mac OS X 10.9 through 10.11.2.
Does not affect Mountain Lion 10.8 and below on the tested system.
Series GPU tested: Tesla Architecture (NV50 series)
320m (like GT218, but integrated) (320m is also the last revision of the tesla arch, so the entire tesla family from 2006 to 2010 is probably affected)
After countless hours of debugging with an opengl driver monitor, I've seen the commands issued by your game. Your game is lacking glFlushes and/or when it's calling swapBuffers, it's not causing the commands built up in the driver to be sent to the GPU. I'm seeing the driver wait til its internal arenas for command queues is built up before sending them off to the GPU.
Some Possible Fixes:
1) Update LWJGL to version 3, version 2 is severely out of date and might not be causing a command queue flush on Mavericks and up with its abstracted version of swapBuffers.
2) (Probably the easiest immediate fix) Insert glFlush/glFinish commands to hopefully force the driver to send your built up commands after the end of a frame's worth of opengl commands.
This bug is not a VRAM usage limitation (Even though the GPU this is running on is 256 megabytes "shared", also the OS pages more if need be, windows for instance starts it with 1 gig), as it occurs independent of the amount of free VRAM. I made sure to monitor VRAM levels as a trigger for this issue. The jank only starts in SK when the nvidia driver (confirmed via spindump for driver time in kernel process) in kernel_task spikes and SK in accordance drops in CPU usage. After using the official OpenGL Profiler and OpenGL Driver Monitor provided by the Apple Developer website, it appears to be related to the lack of proper flushing of commands to the GPU when it should occur.
There is a chance LWJGL's swapBuffers might be telling the GPU the ordinary swapBuffers command (OpenGL driver monitor isn't reporting swapBuffers directly, only Apple related events for swapping), which "should" force opengl command flushing to the GPU, but the Nvidia driver for OS X (Apple placed tesla arch cards with their own geforce tesla driver now on mavericks+ separate from fermi cards) is not recognizing it. The jank when it happens gets worse as the client runs and occurs after multiple levels loading 10+ minutes in.
Someone at the company probably should get a Mac with a Tesla architecture card (One that has OpenGL 3.3 access, but not 4.X), and run Mavericks or higher on it with SK. The game was tested against older OS X before the driver got updated and did things differently for Tesla type cards circa 2013. Doesn't matter it's opengl 3.3, since SK requests only legacy OpenGL 2, which cards from the year 2003 support.
Now I'm wondering if the render to textures like the character portraits and item 3d displays (helmets and armors) are missing some opengl flush/finish/sync-object. I'm getting glitches on mavericks+ for them, but not in mountain lion where there is no jank issue. Seems like the opengl state is not rendering fully when the framebuffer is swapped for sure, whether it's sk's fault or nvidia driver's fault. I'd recommend at the very least for someone at OOO to sneak in some synchronization calls for compatibility mode at the very least. I also see glitched player portraits in most screenshots from other players out there, so I wonder if there's a chain reaction of glitching in the driver from the lack of synchronization for something specific like that.