The brew boiler overheats, about 15C above the target, from a cold start. This speeds up heating the group, since it ups the thermosyphon temperature. If you restart the machine before it has cooled down, it does not do this. I've found that when the display stops flashing after a cold start, the brew temperature is right; but not after a warm start, when it is often too cool, and it is better to wait an extra few minutes.
The easiest way to check is to take a naked thermocouple and use an insulated pad to press it against the neck of the group. When the neck reaches the temperature you've programmed for the shot, everything is good. In general, on E61 groups, the neck temperature is roughly equal to the shot temperature.