The problem was the Service Manager's startpath was pointing to the wrong agent:
The FTP Agent was starting with:
- 'java -jar -Xmx256M E:\Automic\ServiceManager\bin\..\..\Agents\RAFTP\bin\ucxjcitx.jar disable_cache'
but the start directory was:
- 'E:\Automic\ServiceManager\bin\..\..\Agents\sql\bin'.
Automic Admin updated it to the following, which resolved the problem:
- 'E:\Automic\ServiceManager\bin\..\..\Agents\RAFTP\bin'.