Prompt When Ejecting Time Machine Drive
Could it be that there is a hidden partition available on that drive?

Disk Utility can show hidden partitions, but be default it doesn't do this. You can enable this feature by first enabling the program's "Debug" menu. Just enter the following command in the Terminal, which will edit the Disk Utility preferences file accordingly:

defaults write com.apple.DiskUtility DUDebugMenuEnabled 1

Now relaunch Disk Utility and you should be able to see the hidden partitions by choosing "Show Every Partition" from the now-present "Debug" menu. Do keep in mind that editing hidden partitions may not be a good idea in most situations.