You need to kill it? Why is that? You get just a black screen?
I'll try to test tonight, strange.
You didn't told the model of Pandora you are using?
Not even a black screen... the mouse cursor disappears and nothing in gui changes, but I can't interact with anything. Even pressing the Pandora button won't bring up the menu. I have let it sit like that for minutes but the only way to get any control back is to press and hold Pandora butoon until it reloads the desktop (what does that do anyway? obviously not restarting X since the other open apps come back where they left off).
This is on a Rebirth with no overclocking enabled.
I have the same kind of problems. Haven't tried with emulators, but with Super Methane Brothers, Valyria Tear, Super Maryo Chronicles and somesuch. For Valyria Tear, I get a black screen and the music, but no interaction (have to kill with pandora button). For SMB, I get a strange noop - The program starts, it visibly opens a window and full-sizes it, but the window contains an image of the desktop, so I get what seems to be nothing happening at all (an image of the desktop on top of the desktop). Also music, also has to kill with pandora button. SMC goes black and crashes - Needs Pandora+power switch. Rebirth, no strange display driver, no more than 800Mhz on the clock.
I've not tried a full reflash so far, only the "update system" thingie. Only SMB left anything useful in the pndout, however, that was complaints about not being able to create GL stuff, if I remember correctly.
Will fiddle with SGX installer to see if it helps.