I wonder why it is doing that.  Do you have a docklet that is reading or looking for the USD drive?

Do you have a docket setup to show you the system tray icons. If you have one it should show the system tray icons and the remove the hardware saftely icon on there. That way you should just have to click on that icon and remove the drive. Have you tried that. I made a dock on the bottom right with no icon on it then went to dock contents and enabled  the option that says display system tray icons along with my icons. that way it will work just like the windows system tray then another thing you can do it to make the dock invisible by making it totally transparent.  Another thing that I did is in the positioning options window click on hide in background when not in use then set the delay to short. This way if you have a window maximized you can place your mouse over the spot where the systray dock is and bring it to the front so you can click on the remove safely icon from right there without having to exit anything. If you need any help on setting this up let me know. . This program has a high learning curve for the fancy things but when you know how to use full potential of this program its a real time saver belive me. Im happy as hell with this thing. .