Late to the party, but......
I recently purchased a iMac G5, 1.6 PPC and I upgraded to 2 GB RAM. I noticed the same issue with the dock. I first tried to do a clean install with Leopard 10.5.1 without success. I added the second gig of memory, again without success. I did the command line in the terminal as suggested in prior posts. I did not however install the additional tools, mainly because I couldn't figure out how. But, just by using the command line it rectified 99.5% of the issue. The animation is smoother and when it auto hides is better too. I do have a slight issue when I first unhide it but it seems to fix it.