Which version of LWJGL are you using? Could you try the latest (1.1.4 and 2.0a2) if you haven't already? Leishy: Which linux distribution and version are you using, and could you try the standard KeyboardTest from lwjgl? raft: I can't reproduce the problem here, on a Ubuntu 7.10, so to get any further, you'll need to dig down yourself. The interesting code is in java (for example, see if LinuxDisplay.processEvents() gets any events when pressing ctrl, and if so, why they don't end up in KeyboardTest) so you should be able to compile a custom version of LWJGL (or use a debugger).
- elias