Finally I found time to test the whole thing again (work has been biting very hard), and as Gerrykeely said, the problem is on the RTS and DTS lines that are pulled down by the arduino IDE terminal putting the ESP in bootload mode.
I'm trying to find a solution to maintain those lines connected to use the auto loading capacity of the Arduino IDE, and disabling those lines on the terminal (if it can be done???!!).
Until then I have to disconnect the control lines after loading.