For certain Java applications, when they are started through the 'Run Application' action, it seems to make their captured Controls inaccessible for the rest of the Process, when executed outside of the Process Designer (run through WA Console, schedule-trigger or Compiled).

As a workaround, replacing 'Run Application' with 'Run DOS Command' to launch the executable of the application resolves this issue and allows the rest of the Process to access the Controls of the application.