Does your membership plugin or any other plugin also perhaps have a new registration email option?
The way that WordPress allows for this is known as a ‘pluggable function’. WP obviously has it’s own function to send emails but before it is loaded and used it checks to see if there is another function with the same name – which would be supplied by a plugin. If found it runs that one instead.
So – if two plugins both supply alternative functions with the same name it is going to be down to chance as much as anything as to which one gets loaded to replace the WP native one. It becomes a lottery really. So if you DO have another source of a new user email it could just be wining that content and being used insread of the SP replacememnt one.