I have assigned WSE and salinity time series to 38 South boundary cells following the tutorial. After executing the model, salinity at the boundary is applied only at one cell (the cell farthest to the East). EEMS seems to ignore the salinity time-series for all the rest of the cells in the boundary group. I am using EEMS 10.3.10. Your help will be greatly appreciated.
Recent versions of EEMS have not had any issues such as you describe. There was a bug fix for EEMS 11.4 that addressed an issue where the flow assignment for all time series did not work properly, but this may not be what you are describing. If it is a bug then you will need to upgrade to get the updated version.