Users with Microsoft Windows Vista and an iPod may have encountered issues with data on their device becoming corrupt after they have connected it to a PC running Windows Vista. According to Microsoft, the problem can arise under two circumstances which I pasted below:
Both surely look like the normal way to remove an iPod from the PC. Microsoft makes no mention if this is also happening when you just disconnect the iPod without using the safely remove feature or eject feature.
When you try to disconnect an iPod from a Windows-Vista based computer, the data on the iPod may become corrupted. This article describes how you can download an update that prevents this problem from occurring in the future. Note that the update addresses only the issue in which the Eject command does not work when you right-click the iPod through Windows Explorer or when you use the Safely Remove Hardware icon in the notification area. If you are searching for troubleshooting information that is not referred to in this article, please try searching the Knowledge Base again by using keywords that describe your problem. This article provides step-by-step guidance that leads you through downloading the update and how you can prevent this problem from occurring.
You can download two updates, one for the 32-bit version of Windows Vista (click for direct download) and one for the 64-bit version (click for direct download)
Update: The issue is not a problem in newer versions of Microsoft's operating system. If you are running Windows Vista, make sure you have the latest service pack for the operating system installed as it contains the patch needed to fix the issue.
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