Try reinstalling with the 7800GT in. My MDD with a 7800GS was slow as hell, no better than the Radeon 9000 that was in there before. I thought it might be a driver issue and reinstalled the OS and it was much, much faster. I did also install Tiger instead of Leopard but if anything Leopard should have better support for these newer cards.
Nvidia Geforce 7800 AGP - The Mac Elite

scroll down, there is a patch for 10.4.9