Hi Robert,
For this add-on to identify a folder as Junk or Trash, it must be configured as such.
In the 'Account Setting' for a given account,in the 'Server Settings' there is a set of radio buttons under heading 'When I delete a message:". One of the radio buttons is 'Move it to this folder:'. Make sure that folder correctly points to trash.
Similarly in the 'Junk Settings' tab, under the heading 'Destination and Retention', make sure the Junk folder pointed out is correct.
Additionally, in 'Add-ons Manager -> Empty 'em -> Preferences', make sure 'Include Trash folders' and 'Include Junk folders' are checked. You could try checking the "Override folder's confirmation setting' option.
If you need further debug information, set 'Enable console debug messages' in Empty 'em preferences and monitor the Error Console when you click the Empty 'em button.
Just as a note, if you newly configure Thunderbird with multiple accounts with lot of email to download, the tasks may be queued. It may appear that Empty 'em is not emptying Junk/Trash folders. Give it some time.
Hope this helps.
Thanks,
Mahesh.