Hi,
Firstly, please make sure you are using the latest FTP Voyager release, version 16.0.2.0. If the issue persists, continue as below.
FTP Voyager 16 establishes a separate set of Site Profiles for FTP Voyager vs FTP Voyager Scheduler. This mitigates many issues that would occur with Site Profile Management in older releases of the product. If you are seeing authentication errors in FTP Voyager Scheduler where you do not in FTP Voyager, most likely the password was updated in the GUI application profiles but not in the Scheduler profiles. To address this, go to "Tools | Scheduler Site Profiles" and edit the Scheduler-side profile with the correct password, and Connect to it at which point you should be able to schedule tasks for that site with no issues.
Hope this helps!
Thomas Parikka