When i try to put Minecraft in fullscreen mode in Linux, the window gets transparent and i can't do anything. I must to press Alt+Tab to move behind the windows and close the game. However, to put again the game in Windowed mode i need to edit the Minecraft config file manualy.
Thank you.
[EDIT 2/9/2014]
The problem is still here with 1.8, but now the fullscreen mode works sometimes.
[EDIT 29/11/2014]
In 1.8.1 the problem is still present.
[EDIT 3/2/2015]
With OpenJDK 1.8 and Minecraft 1.8.3-pre6 the problem is not fixed...
[EDIT 20/12/2015]
This bug is still not fixed on 1.8.9
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I am having this problem in 1.8 pre-3 using mint
Currently i'm using Ubuntu 14.04 to play Minecraft 1.8 but the problem is still there.
I updated the affected versions and added more information.
Thank you.
Updated once again...
Please do not mark unreleased versions (anything starting with "Future Version") as affected. You don't have access to them yet.
Switching to and from fullscreen works fine for me, but the window continues capturing clicks, etc. even when alt-tabbing to another.
If someone knows how to report this LWJGL issue on GitHub i appreciate it. If this is not a LWJGL issue, please make a research for fix this bug.

This comment of a LWJGL developer should probably be added
The Windows (super) key also triggers this. It would be better if this key simply did nothing in Minecraft. Valve's games ignore the key, for example.
Can confirm for 1.9.4 and 1.10-pre1.
Additional information: it's only happened to me in my Ubuntu 16.04 installation when pushing the "Super" (Windows) key, which visually minimizes Minecraft and brings up Unity's search popup, but leaves an invisible Minecraft behind. F11 works as intended, as does quitting normally.
The way it works is that the window simply turns invisible. Keyboard action controls the stuff in the background, yet clicking only controls Minecraft, meaning that if you're careful you could blind-click your way to the title screen and quit. (I successfully tested this.) Another temporary fix is to do Ctrl+Alt+F2, from which you can run "killall -9 java" to kill all running Java, including the bugged-out Minecraft, and after which Ctrl+Alt+F7 returns you to your desktop. At least that's how it works in Unity; I haven't run any other desktop environments yet so I can't speak for any others.
Is this still an issue in the latest snapshot 16w44a? If so please update the affected versions.
This is an automated comment on any open or reopened issue with out-of-date affected versions.

Can someone please check if this is still an issue in the latest snapshot 17w43b?

Mine seems to work now (both in 17w43b and 1.12.2), but it could also be that I just updated to OpenJDK 1.8.0_141

Snapshot 17w43a updated from LWJGL 2 to LWJGL 3, which led to a bunch of bugs like this getting fixed, so if it works for you and didn't work in 1.12.2, then it's probably fixed now.

Oh, hm. Good point. It looks like this was actually an LWJGL 2 issue as per comments from the LWJGL devs here, with that actual fix never being merged (as far as I can tell). So, it's hard to tell exactly whether this was fixed earlier or not.
But the actual LWJGL bug should no longer be a problem in LWJGL 3, at least. (Correct me if I'm wrong, please, as this isn't something I'm 100% familiar with)
Is this still a concern in the current Minecraft version 14w30c or later? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.