Right, so I got the code for the extra Specializations, redeemed it, and have had them sitting there, perfectly normal and all is good.
Then today I go to look at them, and there were only 2 of them…what’s happened?
I reached SR50, disconnected my console from XBL to see if they’d show up so I could select one, they showed up for a brief moment then went back to only having 2.
How do I get them back?
Try a combination of clearing your cache, re-downloading and restarting your console.
I’ve found that it sometimes gets them to re-appear, however they do not stay.
It happened to me as well.
It came back after I re-downloaded the cache and specializations.
For anyone that encounters the same problem with missing Specializations, you need to do the following, either:
A) Clear the system cache (like mentioned above) and/or re download the specializations.
B) BE OFFLINE from XBL when you are in need of a new Specialization, load Halo 4 and then go straight to the Specialization menu, choose a new one, and they will stay there for good again 
Thanks for the help guys, hope these fix anyone who has problems in the future!