API returns values of multi-select custom field in different format depending on the entitiy the custom field set is used for.

There is a forum thread about this issue: http://forum.civicrm.org/index.php?topic=35646

If you create a custom fieldset for a contact, with a custom field that is alphanumeric and multi-select, the API returns the values of this custom field as an array. E.g.

{ "contact_id":"1", "civicrm_value_mycustomset_4_id":"1", "custom_7":["A","B"], "id":"1" }

When the custom field set is used for a relationship, and you do the same, the values for the custom field are returned as key-value pairs:

{
"id":"219",
"contact_id_a":"96",
"contact_id_b":"2",
"relationship_type_id":"5",
"is_active":"1",
"description":"",
"is_permission_a_b":"0",
"is_permission_b_a":"0",
"custom_8":

{ "A":"A", "B":"B" }

,
"custom_8_3":

{ "A":"A", "B":"B" }

}