In windows home server 2008, using windows' power saving features. ive always had this problem with windows (xp and 7). the drives will spin down after the allotted time, but then spin up a matter of seconds or minutes later even if the drive isnt being accessed. im assuming theres some sort of background work being done by windows that needs to be turned off (indexing? caching?), but i dont know what it is. ive noticed the drives are also very noisy when they park. this is how i know they arent staying spun down because they "clack" loudly every few minutes when the heads park.
Indexing and defragmentation are the most likely causes. Indexing can be en/disabled on a drive-by-drive basis by right-clicking on the drive in Windows Explorer, selecting Properties and checking/clearing the "Allow files on this drive to have contents indexed..." box at the bottom of the dialog box. See here to disable defragmentation on Win7/Vista. If drive activity persists, then download and install Process Explorer. Aside from providing shedloads of information on individual processes, it also provides useful charts for CPU, memory and IO usage. Examine the IO charts to find what processes are accessing the disk and take it from there (anti-virus software running background scans being one likely culprit). Drives shouldn't be noisy (at least, not any released in the last decade or so). It may be worth backing up the data on them and checking for hardware problems.
My F1's while and click when they shut down, so it's fine. I like it as you do it in sequence so it's like a countdown to power off My guess is AV, as it'll start scanning when ever you leave it idle, so just disable that and run a scan once a week... Or get a small SSD as a OS drive, then the other drive wont usually be accessed much (I've noticed this on my rig now I have mey SSD's)