Minecraft – How to fix Minecraft being off-center

I have a very annoying issue that is making my Minecraft experience, as well as any other games using LWJGL as an engine.

This is what my Minecraft looks like:

As you can see there are black bars there, and it also seems like the mouse doesn't line up with the buttons – as if the buttons are there in the black area but visually off.

This also occurs when the window is resized:

Same issues. Black bars also seem to remain here.

This occurs with other things that use LWJGL as well, such as CCEmuRedux (a ComputerCraft emulator that uses that engine).

Going fullscreen in MC does fix it but the issue returns when exiting from fullscreen. I have tried this already.

This is my system report: Pastebin link
For those that think that is too long, here is the summary: Windows 10 Insider Preview, latest version. NVidia GTX 660 SC EVGA, with the latest NVidia Windows 10 Driver. Java 8 latest version, x64.

Thank you for helping me.