The problem occurred when users tried to eject an iPod through the 'safely remove hardware' feature in Vista.
Using the feature could cause the iPod to become corrupted, requiring all music and video content to be reinstalled.
The fix marks the close of a tumultuous start for iPod users running Microsoft's new operating system.
Users reported the corruption issues shortly after Vista's release, including being unable to make any changes to their iPods or access songs purchased through the iTunes Music Store.
Sluggish performance of Apple's Cover Flow feature was also reported.
Apple issued an advisory warning users not to upgrade to Vista until the issues could be resolved.
An update in early March fixed several of the compatibility vulnerabilities, but Apple warned users that the 'safely remove hardware' feature could still cause problems and recommended that users eject the iPod through iTunes instead.
The update is one of 10 minor patches for the x86 and x64 versions of Vista issued by Microsoft. Other patches include fixes for compatibility issues with Canon cameras and a problem with Vista's PPP dial-up internet component.
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