I'm having the same issue. It does this occasionally, usually after rebooting the system. I'll load the AceKard's interface, navigate to the emulator, then when it runs, it's as though the system just locks up. Nothing happens, no input from any button or the touch screen can elicit a response. I have to shut the system down completely, then restart it (or just a soft reset since this is a DSi). When it DOES work, it works wonderfully...but it's maddening having to fight just to get the device to work. Nothing seems to change between when it will and will not work, I have not moved any system folders or files. I have not relocated the roms, I have not done anything except turn the system on and off throughout all my attempts to run the emulator.
Is there a patch or an updated version that corrects whatever problem this is?