Missing menus from SPRO after a SAP All In One install

Hi guys hoping someone could point me in the right direction on this one.

About a year ago I build 3 SAP AIO systems (one being dev, another being UAT, last being Production).

The way I installed was to use the manual on all 3 systems and not to install the base and then transport modifications over, the reason for this is that it seemed the safest way. After about 12 months a have had a user come back to be and say that the UAT system and the PROD systems are different and that the PROD system is missing the following menus under the Logistics - General menu in IMG

The missing items in the production system are

Article Hierarchy

Generice Hierarchy

Price Level Groups.

I have check SFW5 in both system and both of them have the same options selected in the Business Function Status's

As I have been out of BASIS for almost 12 months I have no idea where to look here to see which part of the install didn't work.

I think a good start would be "Does anyone know how I could be missing menus out of IMG when the Business Function Status are correct"?

One last thing is that Production isn't live yet, hence why they have only just found it.