No, that would be innefficient, I think... How would it know what to load up?
I was thinking was that the light would light up for a half a second or so and you hear the drive kicking in and such... but if it goes on for minutes without you doing anything, then that's troubling.
If you think that it could be a spyware program running or something and you have more then one computer on a network, you could setup a packet sniffer on the second computer and see if your computer is being accessed over the network. (it'd work on a wireless network or a network connected by a normal hub... a network with a switch or a router instead of a hub will isolate machines from that sort of thing and make packet sniffing more difficult)
Maybe disconnect your machine from the network and see if it still happens? All I can think of besides that is the normal anti-spyware stuff, check the running programs out, see if there is any weird background proccesses going on, check out msconfig's startup tab to see if any programs are set to start up on boot-up that you don't know about, use virus/adaware/spybot scanners, etc etc etc. (I am sure you know the drill)
But it shouldn't go on and on like that for more then a second or two unless your running out of RAM or are reading/writing files from the disk...