I just completed the MA-6 mission again. Before doing so, I verified my flies on Steam and no issues with files. Also, during times in the mission, I used some time scale up to 20x during "dead" periods. Also, I followed all instructions and used the "Complete Objective" box to make sure I did not miss any important tasks.
Everything seems ok during the mission, but the messages still start to seem out of sync after retrofire has been completed. For instance, the messages that I listed before, like about going into reentry attitude, bypassing the 0.5G switch, and retracting the periscope are all given at times when the spacecraft is just starting the fireball phase of reentry. In particular, the messages about manually retracting the telescope appear only after the periscope was retracted automatically.
I am thinking of going through the mission again, but without doing any time scale at all, but if I remember correctly, you did some time scale in your video about the same mission, so this might not be a time scale issue.
Also, I wanted to talk about the MA-6 Friendship 7 (MCC) mission again. The problem that I discovered was that when clicking on the MA-6 Friendship 7 (MCC) button to open the mission, when clicking Launch, it sends you to the MCC version of Mercury-Redstone 4 historical mission.
In closing, none of these issues prevented me from completing the mission successfully. I found this particular mission extremely enjoyable due to a lot of the interactivity between John Glenn and Mission Control.