After defining the scouts on the cortex of the template anatomy, you need to project them back from the template anatomy to each subject. For each source map for which you want to compute the scouts time series, you need the scouts to be available on the surface that was used to estimate the sources.
The Pipeline editor window only shows the scouts available for the first file in the Process1 list. This creates a batch/script, but then you are responsible for making sure this batch is applicable to all the other files selected in Process1.
If you have too many subjects to do it manually or if you want to script it for reproducibility, you can use the function bst_project_scouts.m.