My jme application allows the user to alter the graphics settings from within the game. After saving the user changes into AppSettings, I use LegacyApplication.restart() to apply the changes. If the user has changed the Samples value for anti-alias, the Gui z-order is screwed up.
I traced the problem back to RenderContext.reset(). There are some differences between what is initially created during instance construction and what .reset() sets.
I am not very graphics savvy and cannot identify exactly the problem/cause. However, if I move all the instance value settings into a method, and call that same method in the base constructor and the .reset() method, the problem goes away.
Hopefully someone out there can apply a proper fix.