I have just spent a good 3 hours trying to solve this and I have found a solution that has worked perfectly for myself. I will try to explain as best I can and its not necessarily the best solution, but it works.
You will need to use the following code for each checkbox field you have in order to fully populate all selected checkbox values -
YOUR_FORM_ID = the ID of the Gravity Form You have created
ACF_FIELDNAME = the exact Advanced Custom Fields Field Name of Your Checkbox Field Type.
ACF_FIELD_KEY = The Field Key of your checkbox Field Type in Advanced Custom Fields. (To get the Field Key open up Custom Fields and go to "Screen Options" at the top of the screen and select "Show Field Key = Yes"
Paste the following into functions.php
add_action("gform_after_submission_YOUR_FORM_ID", "acf_post_submission", 10, 2);
function acf_post_submission ($entry, $form)
$post_id = $entry["post_id"];
$values = get_post_custom_values("ACF_FIELDNAME", $post_id);
update_field("ACF_FIELD_KEY", $values, $post_id);