Hi. I just tested both 1.10.2 and 16w42a.
Unfortunately the issue is still present.
I tried this again using snapshot 16w07a and the issue still exists. No issues on my primary screen, but on the secondary screen the pointer appears outside the window whenever the inventory is opened.
Note: I even deleted all my different launchers all together. I installed the vanilla minecraft launcher obtained from the main website and did a clean install. I loaded the newest snapshot and the issue was still present.
EDIT: I even tried disabling all external devices (including my wireless keyboard and trackpad). Issue is still present.
I can confirm that the bug is still present in the latest snapshot (15w46a).
EDIT: I have also since upgraded my OSX to El Capitan and, as stated before, the bug is still present.
I can also confirm this happens on my multi-monitor setup. However, replication and symptoms are only slightly different, but the same problem nonetheless.
I use an external monitor (2560x1440 resolution) as my primary screen and my built-in retina display (2880x1800 resolution) as my secondary screen.
When playing Minecraft in windowed mode on the primary screen (external monitor in my case), the cursor is always centred in-game when opening inventories, no matter the placement of the Minecraft window on the screen.
Moving the Minecraft window over to the secondary screen (built-in retina), the cursor always moves ABOVE and outside of the Minecraft window. The cursor seems to place itself at a fixed distance above the window no matter the placement of the window itself, but will always correctly center itself horizontally with the Minecraft window.
I tested it on both the latest release 1.12.2 and the latest snapshot 17w49b.
The latest release 1.12.2 still has the issue (Which is why mods didn't ask about testing the release, probably 😛)
But... HALLELUJAH! The issue is fixed on my mac when I run the latest 17w49b snapshot!
Thanks to whoever was working on this!