Dear Dr.Jagannathan,
I think the problem is related to the date you specified for the
change in CO2 concentration. I tested a similar issue in my models. I
saw that where the fertilizer application date is before the planting
date, even if the simulation is run before both of them, the effect of
fertilizer application is ignored. I suggest to check ENVIRONMENT
MODIFICATIONS section and set the modification date to a date after
planting date.

Best
Behnam