So sorry you are dealing with these issues!
That's exactly what happened to me when my protocols were switched. A change in protocol often results in different areas of infection being hit. That means there's always the potential for herxing.
Detoxing will help a lot with this. I'm not sure what you're doing for detoxing but you need to do more - it's our only hope of reducing symptoms.
Here's a link to a thread wherein members shared what they are doing for detoxing:
www.healingwell.com/community/default.aspx?f=30&m=3602759Maybe you can add a few things to your detoxing protocol and continue to add to it.
You need to stay ahead of the killing.
Good luck!!