After attempts to format, fdisk /mbr, diskpart clean, etc. all failed. I did some poking around and found the uninstaller is bundled with the startup app, clever...
- Insert your U3 flash drive and Launch the U3 application.
- Click on the U3 Launchpad Settings
- Click the Uninstall tab on the Settings menu (all windows and files accessed from the flash drive must be closed).
- Finally, click Uninstall U3 Launchpad
That's it, no more pop-ups and annoying software.