Hi Zsuzsi,
No need for -D for your design as long as you include the intercept, which you are already including (EV1).
The results that you describe seem fine, just that there is a global effect in C2, and nothing in the opposite direction (C3).
The C1 isn't necessary, and it's the one that is causing those warnings when you include the -D (the warnings should disappear if you remove the intercept and then add the -D, but that's not necessary; just carry on with the intercept in the model, without -D, and dropping C1).
All the best,
Anderson