Hi, thanks for the detailed information. First try updating to 3.2.2 that was just released. I did find a bug reading one of the output files, so it could be that. After updating, go to the Run page and re-run just the Analyze output for visualization part to re-read your output.
This version does update SWAT+ Check so it will look a bit different. There is still one place where NA exists due to current unavailability, and in the updated version that is under Plants tab, Removed in Yield; Nitrogen and Phosphorus.
If other things still don't look correct, you can look at the outputs directly in your TxtInOut, the basin_nb_aa file in particular for nutrients.