The difference between DDR and DDR2 probably has no bearing on why the graphics card doesn't work. That system is old enough that if it has a graphics slot, it's probably AGP.
Nope in looking at the tech specs for the Dimension 1000 it only has 3 PCI slots !! (No AGP or PCI-e slot ata all) - for your system you will need a PCI video card and they are not very good for gaming - and are much more expensive than the same card in either AGP or PCI-e version !
What 8400GS did you buy ?? - is it the PCI version ? - If not that would be why it does not work - if it is did you also go into the BIOS and disable the onboard video as well as set the primary video source to initialize the PCI slot ?