Hi Mary,
The recent version of pmx (develop branch) applies a scaling factor of 0.33 by default. Hence, the DUM_C has a mass of 12.01*0.33=3.9633. The web server uses an old version of pmx, in which the mass of a dummy is 1.0 by default. The scaling factor is used to maintain the stability of a simulated system.
You can read this thread for more on the discussion: Oscillational period warning during tripeptide A2I forward simulation
Using either of the itp files should be fine provided that your simulation is stable (no oscillation-period-warning). The mass of the dummy particle will not have much effect on the ddG prediction.
Best,
Sudarshan