Did you use mirror joints to create the other side joint chain? If so, you probably have "mirror behavior" on. This makes it so that when the same joint on both sides of a character are selected and rotated, they mirror each other. What causes that to happen is the joint orient values and the negation of translation values.
Now when you suddenly insert a group node into the result of the mirroring, the group node doesn't know about any of that. You might try creating that group on your initial joint chain and remirroring again. Or you can make a duplicate of that joint that's going to be grouped. And after grouping, orient constrain the flipped joint to your duplicate. Of course. you'll need to break the connection on the flipped joint. Now once oriented, delete the orientConstraint and freeze the rotations of your joint. Also delete the duplicate joint. Now remake the connections. They may have to be altered because everything is different relating to this joint. You might not have the mirror behavior any more. Sorry, I'm not where I can test this out. Just some ideas for you to try. Good luck.
