Dear Carlos,
There is no error in what you see in the output files. It is just water stress (or any other stress) is reported in the SAD and ACY file.
The WS reported in the SAD file is the regulator factor that affects the biomass accumulation for the day. Since it is a multiplier, a high value indicates low stress (1 = no stress, all the potential biomass become actual biomass) and a low value indicates high stress (0 = severe stress, no biomass accumulation on that day). On each day, only the most severe stress affects the biomass accumulation. The column RES has the value of the regulator used to constrain the biomass accumulation.
In the ACY file, the model reports the number of days each stress was the most severe of all the stresses simulated. In this case, a low number indicates a low stress (in your case, low number of days with water stress). To get the WS value reported in the ACY file, from the SAD file, you have to consider only the days when WS was the most severe stress (WS=REG) and sum them as 1-WS.
Let me know if you need more information.
Luca