I've also recently had this problem. I took a long break from N64 emulation stuff because I've already exhausted by gaming on the system, but I wanted to play Ogre Battle again. I gave up yesterday after looking through here.. I tried ending processes and all that good stuff.
However, today I ended up clearing a huge list of running processes (I usually run above 30 processes for no reason other than I'm too lazy to suspend them from starting up originally) I'm not sure which one allowed it to work, but apparently it's now working. I turned off most running processes that were labeled "Owner" and any that I knew didn't need to be run under "System". If that helps anyone with this problem, good. It helped me.
Just giving my input into the problem. Apparently it was one of my processes (It may have been Norton Antivirus, but any assortment of things. I'll do this again next reboot and single which one it was, but for now I'll enjoy the ability of it working)