I can confirm this is still an issue with the latest 1.9 release. I have the exact same setup as Riekman. My external monitor is setup as my primary screen. My built in MacBook Pro Retina laptop screen is my secondary screen. When playing Minecraft on the laptop screen (not the primary, external monitor), accessing chests, inventory, furnaces, etc, will cause mouse issues.
Here are the simple steps to repeat:
1) Play Minecraft on the secondary screen, in windowed mode.
2) Open inventory 'E' (important - don't move the mouse at all).
3) Use 'E' again to close inventory. At this point, mouse movement, clicking, etc will cease to function.
To get it working again one must:
a) open inventory 'E',
b) move mouse back into window area,
c) close inventory.
I can confirm this is still an issue with the latest 1.9 release. I have the exact same setup as Riekman. My external monitor is setup as my primary screen. My built in MacBook Pro Retina laptop screen is my secondary screen. When playing Minecraft on the laptop screen (not the primary, external monitor), accessing chests, inventory, furnaces, etc, will cause mouse issues.
Here are the simple steps to repeat:
1) Play Minecraft on the secondary screen, in windowed mode.
2) Open inventory 'E' (important - don't move the mouse at all).
3) Use 'E' again to close inventory. At this point, mouse movement, clicking, etc will cease to function.
To get it working again one must:
a) open inventory 'E',
b) move mouse back into window area,
c) close inventory.
Hope this helps.