One of three things: You have a bad RAM Module, or a bad RAM socket or one of the modules is not seated correctly in the socket.
There is another thread here about RAM sockets going bad after the install of 10.3.9. Have you recently upgraded?
You can use Apple System Profiler to show you which socket is reading how much RAM> Write this down. Let's call the working socket "A" and the one not working "B"
Now open your machine, and swap the ram socket for socket, making sure to seat it fully down into the socket when you install.
If it all works, then it was bad seating.
If you show half the RAM, but the RAM that works is in socket "B" this time, it's a bad RAM module
If you show half the RAM, but still in socket "A" (i.e. the previously working module from A now does not work in Socket B) then it is a bad socket or maybe a fault introduced by 10.3.9's firmware upgrade. Call Apple. If you don't have Applecare and the machine is out of warranty, you may have a fight on your hands.
Thanks
Trevor
CanadaRAM.com