Hi -  we have a team of 8  who are in a group of their own and then a secondary group.
Whenever they make a comment, their role changes to the secondary group and I have to go in and manually change it again.

This is her secondary group.

That doesn't really explain what the problem is. I never have a problem with secondary usergroups playing that game. I'm wondering if maybe you have a plugin or a manual modification that's causing that problem.

Have you probably set up group promotions? Please check your ACP => Members => Group Promotions and review the Rules if you have any.