I was having this problem with my G5- a MAJOR friggin headache. Turns out a few things fixed it-
in order of importance:
-turn off Virex, Norton’s, and any virus protection scanning during capture!!!
-make sure that all of your HDs have very different naming schemes
-make sure that your external HD is a fast one, with a good cable, and no other devices are on that Firewire
or USB2 bus
-any iChat camera needs to be disconnected
Hope this works for you.