In the taskbar, the "Safely Remove Hardware" icon has 2 ways of removing the thumb drive. 1st is to right-click and on the popup you have to click stop, another popup is displayed, and you have to select OK. The 2nd way is to left-click, and on the menu, select the drive you want to eject.
Currently the eject feature of Portable apps behaves like the right click, where you have to wade through 2 popups in order to remove your drive. I'm suggesting to operate in the much simpler fashion, if at all possible.
well actually currently this is the best option as other eject options available are closed source solutions, We are trying to find ways though.
your friendly neighbourhood moderator Zach Thibeau