A user field in ACF stores the user ID. With a user field that allows multiple selections it stores an array of user ID values. The reason that you’re seeing the wrong value is that the email address is somehow confusing ACF.
Assuming that customer is the ACF field name. You need to use the email address to look up the user id and then insert that id as part of an array. You should also insert the ACF field key value as well. There is information on ACF field keys on this page http://www.advancedcustomfields.com/resources/update_field/
Welcome to the Advanced Custom Fields community forum.
Browse through ideas, snippets of code, questions and answers between fellow ACF users