Dear Jindrich,
I was able to run your input files on my computer and everything looks fine (the model runs without errors, but for some reason it is not printing the final time stamp. Since you want to simulate just one field/subarea, you can sue the included subarea file, where I have removed the second subarea.
Now, we can begin to work on the problem related to the very low soil water content. First, I want to ask you the location of your simulation. Then, do you have information on the observed potential evapotranspiration for your simulated area? Is it close to the simulated value?
Also, do you have information about the average annual precipitation in the area?
These are the first things we can look at if something in the water cycle is off.
Luca