LWJGL Linux Freeze Bug

No helpful output, as this bug does not effect gameplay; however, whenever I look at any screen that is NOT minecraft while it's running, I have a severe freeze bug that renders everything that isn't minecraft essentually useless.
On older versions of minecraft (Where the "Sticky Keys" were a problem) I simply ran a bash script to fix the issue; but, with 1.6.1, I have found no way of updating (or even downgrading to 1.8.4/5, which worked perfectly for me) the files to remove the problem.
Please implement a way to update them in a sane way.