There shouldn't be any follow issues in PvE. Make sure you're using the more recent Jamba and under Jamba > Team > Follow make sure both have the same settings.

If the settings are all the same, make sure that your master is swapping when you change windows. Also, make sure that your keybind is set correctly and nothing is already bound to your follow key, especially if you are using an FTL setup that sends modified keys based on the master window.