Trying to save an image field on a user using services, but for some reason it isn't saving in base64
You need to make two requests, the first you will POST the base64 encoded string of the file which in turn will return to you the file id, at which point you can make the second call to save the user entity with the file id on the field in question. I have a blog post about this here: http://tylerfrankenstein.com/code/drupal-services-file-create-example-json-and-jquery

Here's the gist of it (assuming your endpoint path is api):

// Get the file id...
$.ajax({
  type: "post",
  data: {
    "file":{
      "file": my_base_64_encoded_image_string,
      "filename": "my_image.jpg",
      "filepath": "public://my_image.jpg",
    }
  },
  url: 'https://www.example.com/api/file.json',
  dataType: 'json',
  success: function(result) {

    // Now that we have the file id, save it on the user entity.
    var userAccount = {
      field_picture: { und: [ { fid: result.fid } ] }
    };

    $.ajax({
      url: "https://www.example.com/api/user/" + localStorage.uid,
      type: 'PUT',
      crossDomain: true,
      headers: {
          'X-CSRF-Token': token
      },
      contentType: 'application/json',
      data: JSON.stringify(userAccount)
    });

  }
});