Yes, all of the parts of the base game + making history expansion are present, it's only the parts that come as part of breaking ground that aren't present.
The parts all seem to be there in GameData -> Serenity and there are entries for them in the PartDatabase.cfg
I'll try this again, previously I kept the .zip and just extracted a new ksp build, and the .exe setups for breaking ground, I'll try deleting them all and trying again, watch this space.
EDIT: deleted everything and redownloaded, no change. Parts from the base game and making history are all present, but none from breaking ground. The robotics category contains no parts and all of the stock craft included in breaking ground show errors.
EDIT 2: Found a solution, if I run KSP in administrator mode, the parts show up, I'll change the permissions for the affected files and we should be golden!
EDIT 3: Yep, all is good now, thank-you very much to everyone who chimed in!
ReconXPanzer's post in Breaking Ground DLC: Parts aren't present was marked as the answer