I just repaired my Replicator 2 and, as you can see, the calibration test went well after a few attemps.
I use Simplify 3D to generate x3g files.
In fact, I really think my question is more general and does not rely to a specific printer with a specific program.
In order to have a great result, the one on the right on the photo, I had to set the extrusion multiplier to 1.25. This setting is a bit odd to me because all was going great before winter with the standard setting which is 0.90. I understand what the setting is used to but I do not know why I had to change it (in addition, there is a large difference).
The first reason that is coming to my mind is the room temperature. It is very cold in the room where the printer is located. The hotend thermistor gives a 15°C value before getting warmed up. Could it be the reason?
Thanks a lot for your help and have a great print! 
From left to right, extrusion multiplier set to:
0.90, 1.00, 1.10, 1.20 and 1.25
