If I press the left alt key, my game loop seems to stop, also the mouse pointer changes back to the operating system cursor.
I’ve googled and the suggested solution was “upgrade your LWJGL libraries”. I’m using v2.9.1 that seems to be the most recent, so I don’t think old libraries are the problem.
Am I doing something wrong? Can I change the key to behave just like any other of the modifier keys? Is this a known problem?
You never noticed that? Thats weird…
No, you are not doing anything wrong. At least not more than everybody else does.
Ermm I never noticed that either… I’ll go ahead and see if I can reproduce what happened to you.
This happens to all lwjgl programs.
It was also a great way to enable auto pilot in minecraft for a long time. (Holding a key when pressing ALT and releasing it before clicking the window covers the key release event)
It’s just my second LWJGL based project and the first time I wanted to make use of the left alt key. It’s a bit annoying that the key seems to be unusable, but there are enough other keys left 
Works fine for me.
Then there must be a solution. What OS and LWJGL version do you use?
Arch Linux 64-bit with the KDE desktop.
Just realised I’m on LWJGL 2.9.0.
I’ll upgrade to 2.9.1 and see if that changes things.
Edit: No change with 2.9.1
Are there the ALT (e.g. F4) shortcuts in Linux?
Yes, assuming that they are configured to do that function, which most of the time they are by default.
Yup.
It’s a KDE thing.
Cas 
Nothing happens when pressing left alt :P. (Windows 7)
I’ve got Windows 7, too. So far I thought that it might be a Windows thing which can’t be reproduced with Linux, but if it works on your Windows, there must be a way to get it working on my computer too. At the moment I’m just using a different key for my game.
Left alt key is working with LWJGL 2.9.1. Tested on Windows 8.1 Pro 64 bit, OSX Mavericks, Ubuntu 13.10 64 bit.