Update to nightly. (Read manual on how to enable nightly updates)
Sorry, I should have included that I am already using nightly builds.
Oh, no, I hadn’t seen those (feeling very silly for what amounts to poor googling skills). Unfortunately, that does not seem to have had any affect. (Yes, I restarted the app after modifying the file) I’ll also add that my problems are not just black splotches, but the occasional complete graphical borking of the visible application; that is, pixels showing up in random places all over the window, my menu selection always being displayed as the top-most element in the menu (but only for the ‘Window’ menu), etc.
Is that with both the canvas and the panel? This sounds like a driver/hardware issue rather than a problem with lwjgl… Wonder why it should work on the whole application too, especially when the command line options are set… 
I’ll also add that my problems are not just black splotches, but the occasional complete graphical borking of the visible application; that is, pixels showing up in random places all over the window,
Hmmmm, I already had the same issue a few months ago, it was an ATI graphic card too. It looks I got to solve the problem by fresh installing a good graphic card driver. It's a linux environment, right? You should testing other 3D applications too(e.g Blender 3D).
I’m working in widows
We would like knowing when you have tested other 3D applications too, then if it works or not.
First, I’ll add that Blender3d works fine for me (it’s the only other 3d app I could think of that I have). Second, the sample (jme3) apps run fine. Third, after thinking about this, I remembered that these problems are a recent occurrence. I’d been using jmp for many months now with no problem. Coinciding with the graphical malformations is that now java is crashing regularly and frequently.
Conclusion: I’m doubting the issue is jmp at all, and much more likely my ocd-like need to tweak my computer/software/settings, specifically java related. I had tried to change a number of things such as update java, overclock my gpu ( though I see these malformations regardless of my gpu state) etc.
I’m actually (separately) installing gentoo for other reasons, but I’ll try it there to see if I get different results. My suspicion is that I’ve fubar’d something somewhere outside of jmonkey with all my random messing about. jMonkey is terrific, and I can’t wait to get back to it.
Just one more thing : Do u remember if you enabled the right repositories via Tools—>Plugins—>settings?
The right repositories :
Base Plataform Alpha
jMonkeyEngine SDK Nightly
jMonkeyEngine SDK Stable
jMonkeyEngine SDK User Contribuitions(optional)
Yes, those are the exact settings I have.
Hmmmm. Just now I see the screen shots you’ve posted at your first post. I’ve never saw that issue before. It’s really strange. I really don’t think it’s a jMonkeyPlataform issue, but yout system itself. Does netbeans work fine or didn’t you try it yet? Is it Windows 7 64x Ultimate?
Sorry xD. The first post was posted by another person xD.