As usual, take the time to write up the issue and then keep hunting and you'll eventually find the issue.
It seems there was a subtle difference between Account and Location, the Location didn't have a reverse mapping for a list of all Items, where as the Account did.
@OneToMany(cascade = CascadeType.ALL, fetch = FetchType.LAZY, mappedBy = "account")
private List<JournalItem> journalItems = new ArrayList<JournalItem>(0);
This mapping is not actually used in our system, so I was able to remove it and when I did so EnVers stopped tracking the Account as changed when the Journal's were added.
Hopefully this might help others stumbling on the same issue.