Re: Windows 7 hard drive thrashing regardless of system being idle or in use
Weird, yes exactly.
Excellent post, I wish I had something worthy to contribute but my suggestions are pretty mundane and likely considering all the trouble shooting you've already done a bit obsolete.
First, available disk space left? Still plenty I would presume but an important consideration.
Second, TLC (tender loving care) multiple passes with a Defragger, built-in and maybe even a third party Auslogic makes a pretty good one. As well as perhaps a run of chkdsk c: /r reboot and let it finish all five stages.
Third and I have no idea how much memory you have available so therefore no way of knowing how much paging is going on, I would suggest using the advanced tab under performance options and setting your pagefile to zero using the custom size option zero in both boxes and select the set button. Reboot, go back in and reset it to a value of one and one half times the amount of memory you have installed same in both boxes Initial size and Maximum size. If you have a second physical drive (not a second partition) move the swap file off the system drive and put it on the second physical drive.
Fourth, are you sure the thrashing is due to I/Os, do you have any reason to suspect a problem with the actual mechanics of the drive, although I'm not sure how that would account for the fact that the noise is not present for a period of time unless of course there's an intermittent heat issue and the drive spindle and bearings are expanding and contracting.
Just a few ideas and like I said you've probably already been there and done that.
Yesterday was, Today is, but ahh Tomorrow...mystery, suspense and a promise of hope.

Operating System Windows 7 Ultimate 64 bit
Computer Type Home built
OS Service Pack Service Pack 1
Internet Explorer Version IE9
DirectX Version 11
CPU Type and Speed AMD Phenom II X6 1090T Black Edition Thuban 3.2GHz
CPU Cooling Stock Factory Cooler
CPU Idle Temp 32C
Motherboard Chipset GIGABYTE GA-870A-UD3 AM3 AMD 870
System BIOS Revision Award F5a (beta) 11/15/2010
System Memory Type G.SKILL Ripjaws Series 16GB (4 x 4GB) 240-Pin DDR3 SDRAM DDR3 1333 (PC3 10666)
System Memory Speed 1333 currently underclocked to 1066
System Memory Clocking 7, 7, 7, 20
Video Card Type and Speed Nvidia GeForce GTS 450 1Gig DDR5 DX11
Video Card Cooling stock
Video Card Temperature 32C idle
Power Supply Unit (PSU) Antec EarthWatts EA750 PSU
Computer Monitor Dual Dell ST2320L
Sound Card Integrated RealTek HDA
Speakers Klipsch
Headset/Microphone Altec Lansing
Hard Drive Two Seagate 500 gig SATAII's ST3500418AS ATA
Optical Drives Lite-On DVDRW x2
Keyboard and Mouse Logitech USB Optical
Modem-Router Type Arris MODEL: TM602G / Microsoft MN700
Network Adapter Realtek RTL8102E/RTL8103E Family PCI-E Fast Ethernet NIC
Printer HP InkJet 990cxi
Network Speed WD Passport 500gig USB 3.0 BackupDrive
USB Controller NEC Electronics USB 3.0 Root Hub
Gaming Console Xbox 360
Anti-virus Software Microsoft Security Essentials
Productivity Suite Office Pro Plus 2010
System Install Date 2011-01-25 21:59:23 on this drive
Computer Skill Level Certified Professional
Windows Experience Index 7.2
Favorite Game FarCry (original, 2 sucked)