On both Java 5 and 6 I was able to get some sort of flickering; the flickering Myolp is describing is tearing, from not having the framerate sync to the vertical refresh rate of his monitor. Odd, 'cause I always thought that Java 6 defaulted to double-buffering in it's AWT components.
Anyway, Myolp, you've used an FPSAnimator and set the framerate to 25fps, which isn't a framerate to maintain v-sync with my monitor (75Hz refresh rate), so I got the tearing. By switching to just the plain Animator (and reducing the rotation rate), I was able to get a much smoother spinning quad, without flickering edges.
Ok, now I'm getting somewhere. Testing it on a computer with a CRT (with a 75Hz refresh rate) I've eliminated the effect. However, on my computers with LCD-displays (60 Hz refresh rate) I still get the problem regardless which animator I use. Tried using the plain Animator and the FPSAnimator with a framerate of a multiple of 60 (30, 60, 90, 120 etc). Printing the choosen GLCapabilities shows that I use both hardware acceleration and doublebuffering. The tearing effect is still there.
The effect also occurs in the Gears-demo but not in the Grand Canyon Demo or moving around in the Infinite Shadow Volumes demo. I guess I need to force the application maintain the v-sync, but is that possible in Java?