Sorry, yes, I meant function*s*.
Yes, evaluating that updates the custom.el fine.
I will edebug (probably later) to see why that is not getting executed from within `package-install`.

On Thu, May 21, 2015 at 2:05 PM Artur Malabarba <bruce.connor.am@gmail.com> wrote:
> I edited package.el as per the diff of that commit and eval'd the changed function.

You mean "functions", plural, right? There are two changed functions
in that commit.

Here's something to try. After you verify that the value of the var
was updated but wasn't saved to custom.el, what happens if you
evaluate the following?

     (package--save-selected-packages package-selected-packages)

Does the value then get saved properly?