Re: Minecraft.jar problems
I have been running minecraft since its 1.8 beta (before 1.0 release) in 64-bit Ubuntu w/openjdk-6 and never had the problem you describe in regular minecraft. I have also run it on both 64-bit Ubuntu and Lubuntu that share a common /home partition, but not that frequently because it is a 1 GHz 2 core tablet PC w/10.1" 1280x800 screen. On that or desktop on 32" 1080p HDTV I typically run full screen, not in a window.
The only thing I can think of is that classic X from years ago would typically only focus on the window the mouse cursor was actually on at the time, instead of the last window clicked. So under Openbox Configuration Manager > Mouse > Focusing Windows, make sure that "Focus windows when the mouse pointer moves over them" is NOT checked. Although, if that was checked it would also tend to move keyboard focus. So if it is a laptop, maybe it has something to do with dragging a thumb on the mousepad.
I usually go to less than full screen when switching to a different workspace to check the minecraft wiki in a web browser, because sometimes when I do that full screen, the keyboard does not respond when I go back. But if I just pick up something out of my inventory with the mouse and put it back in, the keyboard works.
The only time I have had the in game mouse cursor freeze is with tekkit (which is a separate minecraft with a bunch of mods added) and not even sure when that happens, possibly when closing the gui for one of the mod tools. But if that happens, I just hit "E" twice (to go into inventory and back to game) and it clears up.
You may want to upgrade lwjgl. v2.4.2 distributed with minecraft occasionally results in stuck movement keys (press key in same direction you are moving to release a stuck key). So I have been using lwjgl 2.6 (most recent is 2.8.4). It is a zip file that involves replacing files in ~/.minecraft/bin and natives subdirectory under that.
i5 650 3.2 GHz, 8 GB, nvidia GTX 550 Ti 32" 1080p | i7-4700, 8 GB, Intel HD 4600/nvidia GTX 765M 15.6" 1080p | etc.