I've had thig game for a few years have dones several updates. I am currently using a system with very recent released packages (Manjaro Linux). I suspect it to be a problem with Java, I'm not sure how to determine its source. I do not see any log files and when I run the program on the terminal there's no debugging information displaying while the program runs.
(But, yes, there's some weirdness with on-click key modifiers, override rules when combined, and platform specific Java GUI stuff.)