Spun off from bug 346156 comment 4, and bug 344249. This bug is present in JEP 0.9.5+g. After loading Java in a window, key equivalents for menu items are not processed as menu events. In most cases, we have key event handlers that pick these up, however a result of this is that menu titles no longer blink when using a key equivalent, and some key equivalents no longer work. Command-comma (preferences) and command-option-H (hide others) no longer function, as we have not bound these to any keys in the application but instead rely on other mechanisms to associate the keystrokes with menu items.
I've just released a new version of the JEP (0.9.6) that resolves this problem. I actually didn't target this problem directly. Instead the fix seems to have fallen out from a significant change I made to how the JEP works with Carbon browsers -- I figured out how to avoid using Apple's buggy keyboard and mouse event handlers for its buggy Cocoa-Carbon interface! See bug 364158, and particularly item #5 in JEP 0.9.6's changelog.
FIXED by checkin of bug 364158.