The only times I've experienced anything similar to this have been when I've accumulated a very long list of downloaded items on the Firefox Downloads list and have begun a new download for the first time after launching Firefox (like after turning on the computer). The HD activity was then continuously on for a while, the computer was extreme sluggish, and nothing seemed to happen. I'm not sure if it was due to Firefox/virus scanner going through all the files on the Downloads list or whatever, but when I cleared the list, the problem disappeared.

I also used to have a custom made program for modding an old game that for some reason drove my virus scanner crazy despite the fact it was perfectly 100% clean. I had to except the program's folder entirely from the virus scanner. Before the exception, it caused similar behavior: the virus scanner reserved the whole HD access time for itself and pretty much nothing else could be done with the HD.

So, I'd unplug the net connection and turn off the virus scanner for a test of seeing if it makes any difference. If something stresses the HD 100%, in modern computers it wouldn't take that much CPU time but it would really slow down anything else needing the HD.