Can you give more details on your system set-up? It is known that there are issues with some Canon cameras and LaCie Hard drives when they are put on the same firewire bus. The best solution is to purchase a PCI firewire card and put your drives on one bus, and then camera on the second bus.
In my own experience this seems to be the worst when combining the GL2 with FW800 drives on the same bus. I’ve done tests and found the only other solution is to use strictly FW400 drives for capture of DV footage.