I had the same thing happen to me with a brand new CoreDuo machine. It turned out to be a problem with the hard drive settings. Somehow they turned from the DMA setting to PIO, that slowed things enough to result in sub par performance. I think there was a thread fairly recently on how to solve this. My solution was to remove the "removable" drive. Also, it may happen with USB external drives.

Here's the full text of the solution post, unfortunately I didn't record the URL:

Solved the problem.
Curses on Microsoft!
I have my music collection stored on the drive I use for the final edit/save from VRD and between the 11th & 14th October I had been trying out various types of scripts in MediaMonkey to set volume levelling in MP3s. After each run of levelling I used another script to clear the info in the ID3 tags.
This high sustained level of disk io activity must have generated enough crc errors to drop the DMA settings somtime in that period.


http://support.microsoft.com/kb/817472


"According to Microsoft
After the Windows IDE/ATAPI Port driver (Atapi.sys) receives a cumulative total of six time-out or cyclical redundancy check (CRC) errors, the driver reduces the communications speed (the transfer mode) from the highest Direct Memory Access (DMA) mode to lower DMA modes in steps. If the driver continues to receive time-out or CRC errors, the driver eventually reduces the transfer mode to the slowest mode (PIO mode)."

"WORKAROUND
To re-enable the typical, or faster, transfer mode for an affected device:
1. Double-click Administrative Tools, and then click Computer Management.
2. Click System Tools, and then click Device Manager.
3. Expand the IDE ATA/ATAPI Controllers node.
4. Double-click the controller for which you want to restore the typical DMA transfer mode.
5. Click the Driver tab.
6. Click Uninstall.
7. When the process completes, restart your computer. When Windows restarts, the hard disk controller is re-enumerated and the transfer mode is reset to the default value for each device that is connected to the controller.
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STATUS
Microsoft has confirmed that this is a problem in the Microsoft products that are listed in the "Applies to" section.
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Windows XP
This problem was first corrected in Microsoft Windows XP Service Pack 2.
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MORE INFORMATION
The hotfix that this article describes makes the following changes:
• In Windows 2000 only, read requests to ATA disks are sometimes issued with a time-out value of 4 seconds. This occurs when your computer resumes from standby. This might cause a disk time-out because drives typically take more than 4 seconds to spin up. This time-out value was changed to 10 seconds.

In Windows XP and Windows Server 2003, this time-out value is always 10 seconds.
• An alternate, less-aggressive policy is implemented to reduce the transfer mode (from faster to slower DMA modes, and then eventually to PIO mode) on time-out and CRC errors. The existing behavior is that the IDE/ATAPI Port driver (Atapi.sys) reduces the transfer mode after any 6 cumulative time-out or CRC errors. When the new policy is implemented by this fix, Atapi.sys reduces the transfer mode only after 6 consecutive time-out or CRC errors. This new policy is implemented only if the registry value that is described later in this article is present.
To implement the alternate behavior (reducing the transfer mode after six consecutive time-out or CRC errors instead of after six cumulative time-out or CRC errors), you must modify the registry as described below after you apply the hotfix.

WARNING: If you use Registry Editor incorrectly, you may cause serious problems that may require you to reinstall your operating system. Microsoft cannot guarantee that you can solve problems that result from using Registry Editor incorrectly. Use Registry Editor at your own risk.

Follow these steps, and then quit Registry Editor:
1. Click Start, click Run, type regedit, and then click OK.
2. Locate and then click the following key in the registry:
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Contro l\Class\{4D36E96A-E325-11CE-BFC1-08002BE10318}\0001
3. On the Edit menu, point to New, and then click DWORD Value.
4. Type ResetErrorCountersOnSuccess, and then press ENTER.
5. On the Edit menu, click Modify.
6. Type 1, and then click OK.
Follow these steps, and then quit Registry Editor:
1. Click Start, click Run, type regedit, and then click OK.
2. Locate and then click the following key in the registry:
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Contro l\Class\{4D36E96A-E325-11CE-BFC1-08002BE10318}\0002
3. On the Edit menu, point to New, and then click DWORD Value.
4. Type ResetErrorCountersOnSuccess, and then press ENTER.
5. On the Edit menu, click Modify.
6. Type 1, and then click OK.
Note The numbered subkeys that are listed earlier correspond to the primary and secondary IDE channels on a computer that contains a single IDE controller. If your computer contains two IDE controllers, the numbered subkeys for the primary and secondary IDE channels for each of the two controllers may be:
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Contro l\Class\{4D36E96A-E325-11CE-BFC1-08002BE10318}\0002

HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Contro l\Class\{4D36E96A-E325-11CE-BFC1-08002BE10318}\0003

HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Contro l\Class\{4D36E96A-E325-11CE-BFC1-08002BE10318}\0004

HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Contro l\Class\{4D36E96A-E325-11CE-BFC1-08002BE10318}\0005
To verify that you have located the correct subkey, verify that the DriverDesc value for the subkey contains the string value "Primary IDE Channel" or the string value "Secondary IDE Channel."
APPLIES TO
• Microsoft Windows Server 2003, Web Edition
• Microsoft Windows Server 2003, Standard Edition (32-bit x86)
• Microsoft Windows Server 2003, Enterprise Edition (32-bit x86)
• Microsoft Windows Server 2003, Enterprise x64 Edition
• Microsoft Windows XP Professional
• Microsoft Windows XP Home Edition
• Microsoft Windows XP Professional for Itanium-based systems
• Microsoft Windows 2000 Server
• Microsoft Windows 2000 Professional Edition
• Microsoft Windows Small Business Server 2003 Premium Edition
• Microsoft Windows Small Business Server 2003 Standard Edition
• Microsoft Windows XP Tablet PC Edition"

DMA settings for the drive are back to UDMA6 from PIO and FPS processed has jumped to over 650.

HyperReality's suggestion was on the mark even though everything showed as still being in UDMA 5 mode.
Pat's suggestion of a speed of transfer test confirmed the problem as I/O was running 2.5 Mb/s.
Thanks for suggestions and help, maybe this will be of use to others over time.
Last edited by hayden : 10-19-2006 at 08:28 PM.