512 mem doesn't sound like a much memory for what you are doing - 512 is your total Ram? And you shouldn't have to reboot Linux for any reason - at most, kill your X and restart it. Maybe you do have some kind of hardware problem - if so, it would probably be the memory.
You probably just need more memory, but don't quote me on it.
Does EqEmu still use 256k memory per zone? As your players go into different zones, more ram memory gets taken up, and your system probably starts to depend heavily on you swap partition, which will slow you down, big time.
Are you using X while you run eqemu? maybe if you could run the server with loading windows, that would free memory for you.
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