According to a knowledge base article (#936824) posted yesterday on Microsoft's Help and Support Web site, Vista's Eject command doesn't work with properly with a connected iPod and can cause data corruption (see Techmeme discussion):
The Safely Remove Hardware feature and the Windows Explorer "Eject" command do not work correctly with an Apple iPod that is connected to a Windows Vista-based computer
Consider the following scenario. You have an Apple iPod that is connected to a Windows Vista-based computer through a USB connection. Then, you disconnect the iPod from the computer. In this scenario, the data on the iPod may become corrupted. This problem may occur if you use one of the following methods to disconnect the iPod:
• You use the Safely Remove Hardware feature in the notification area to disconnect the iPod. Then, you disconnect the USB cable. • You use the Eject command in Windows Explorer to disconnect the iPod. Then, you disconnect the USB cable.
Apple first reported the Vista data corruption problem in a knowledge base article dated January 26, 2007 (iTunes and Windows Vista Article ID: 305042).
The solution is to download and install a patch for Vista that addresses the problem: