Still having this issue as well. I have tried replacing the same files with versions 3.3.1 and 3.3.3... except for the lwjgl_util.jar which is apparently deprecated since the release of 3.0, even though Indie Stone appears to include lwjgl 3.2.3 for the other files, with their 41.78 release on Linux.
I have added the XMODIFIERS="@im=null" to my startup script. I have turned off repeating keys in gsettings (gnome/mate) and using xset -r. I do not have this problem with other games on linux or PZ in Windows dual boot i.e. same hardware. It's a USB wired keyboard.
It's hella frustrating as it makes it very easy to die in a key moment.
** Also, I found this. I believe that TIS may need this solution **
http://forum.lwjgl.org/index.php?topic=6827.0
