MySQL not outputting all Emojis in text field when using UTF8MB4

We have a project where we're storing Facebook and Twitter posts in a Mysql database, as first almost all Emojis were being stored as ?. We've since gone ahead and made some configuration changes to the database server, and since then we're starting to see more Emojis saving and appearing correctly, however some Emojis are still showing as ?, sadly I'm not sure which ones they are. I know one of them was a basket ball.

When I execute the following commend on MySQL;

SHOW VARIABLES WHERE Variable_name LIKE 'character\_set\_%' OR Variable_name LIKE 'collation%';

I see the following settings;

character_set_client     = utf8
character_set_connection = utf8
character_set_database   = utf8mb4
character_set_filesystem = binary
character_set_results    = utf8
character_set_server     = utf8mb4
character_set_system     = utf8
collation_connection     = utf8_general_ci
collation_database       = utf8mb4_unicode_ci
collation_server         = utf8mb4_unicode_ci

Our database server is hosted with Rackspace, we've asked them to set up the following configuration;

[client]
default-character-set = utf8mb4

[mysql]
default-character-set = utf8mb4

[mysqld]
character-set-client-handshake = FALSE
character-set-server = utf8mb4
collation-server = utf8mb4_unicode_ci
init-connect='SET NAMES utf8mb4'

I think I've narrowed the issue down to the server not applying the init-connect that's defined in the server configuration. If I open mysql workbench and query the database, I see question marks in place of emojis, however if I run the SET NAMES query first, then the subsequent results come back showing the emojis as I expect.