If the graphical version of SpiderOak One or Groups is set to ask for a password at startup, then SpiderOak will likewise ask for a password when running from the command line. On Mac and Linux, this works as expected. On Windows, providing the password on the command line sometimes fails. There are two solutions to this problem; use whichever is more convenient for you.
You can prefix each command with cmd /c. So for example the command to clear the SpiderOak One queue becomes:
cmd /c "C:\Program Files\SpiderOakONE\SpiderOakONE.exe" --destroy-shelved-x
Alternatively you can temporarily disable the need to enter your password. Open the application, go to Preferences - General, and deselect "Ask for password at startup". Press OK. When you finish with this immediate need remember to re-enable this option if desired.