Thanks for the advice and the references.
I'm still getting similar results, but checking my temperature data, I've realised that most minimum temperatures below 0 degrees are characterised as nans in the input weather data, probably due to the range of measurements of the devices. I wonder if that might be a reason for such a bad representation of simulations even adding elevation bands.
Also, I checked out that adding elevation bands during the development of the model with Qgis gives similar results in the .sub files than if adding them later using the utility programs from swat-cup.
Anyway, I'll keep digging into the issue and if I have any good news I'll let you know.
Thanks again for the help.