For the brief time you are at temperature (650) you are not annealing the brass. For that short of time you need to go much higher in temperature. A very good article that describes temperature for dwell time go here
(about half way down).
I use a 650 degree Tempil stick and make my mark below the shoulder. By the time this region gets to 650, the neck is much hotter. You get the brass color change and the neck is much softer. From the linked article:
"The critical time and temperature at which the grain structure reforms into something suitable for case necks is 662 degrees (F) for some 15 minutes. A higher temperature, say from 750 to 800 degrees, will do the same job in a few seconds. If brass is allowed to reach temperatures higher than this (regardless of the time), it will be made irretrievably and irrevocably too soft."
Using a 650 degree indicator in the neck, just stops the heating too early given the short time at temperature necessary to prevent any softening of the brass near the head.