I have two same extension but both are using for a different-different purpose.
Extension A Config.xml
This is the same issue which i faced ,Currently you are adding before tag only in one extension so remove this line.
fee
you have to set the after and before tag in both of the extension.
In Extension A Config.xml file use this
subtotal,discount,shipping
tax,grand_total
and in your Extension B Config.xml file use this
fee
tax,grand_total
Hope this will help yours