Calculated Fields not updating on $bean-save()

Question

Hi all. 
 
 I've been racking my brain on this one now, I tried $bean->updateCalculatedFields(); but it's not working. Currently I am filling in missing records, so I am creating: Lead -> Contact/Account -> Opportunity -> Meeting, they all have a "unique" ID between them that is generated. On all modules apart from the Lead it is a calculated field. But when adding the links between the modules and doing a $bean->save() it's not actually adding the calculated fields in. 
 I tried another save after the fact as well but had no luck. Here's an example of the creation: 
 //Create Account
 $account = BeanFactory::newBean('Accounts');
 $account->customer_salutation_c = $title;
 $account->customer_first_name_c = $firstName;
 $account->customer_last_name_c = $lastName;
 $account->first_name_c = $firstName;
 $account->last_name_c = $lastName;
 $account->name = "$firstName $lastName ($firstName $lastName)"; //This matches formula on leads
 $account->gender_c = $gender;
 $account->date_of_birth_c = $dateOfBirth;
 $account->age_c = $age;
 $account->billing_address_street = $street;
 $account->billing_address_city = $town;
 $account->billing_address_state = $county;
 $account->billing_address_postalcode = $postCode;
 $account->phone_home_c = $phone;
 $account->phone_mobile_c = $mobile;
 $account->email1 = $email;
 //$account->a_branch_accounts_name = $branch; //Should link branches automatically
 $account->created_by = 1;
 $account->save();
 
 //Create Contact
 $contact = BeanFactory::newBean('Contacts');
 $contact->salutation = $title;
 $contact->first_name = $firstName;
 $contact->last_name = $lastName;
 $contact->name = "$firstName $lastName"; //This matches formula on leads
 $contact->gender_c = $gender;
 $contact->date_of_birth_c = $dateOfBirth;
 $contact->age_c = $age;
 $contact->primary_address_street = $street;
 $contact->primary_address_city = $town;
 $contact->primary_address_state = $county;
 $contact->primary_address_postalcode = $postCode;
 $contact->phone_home = $phone;
 $contact->phone_mobile = $mobile;
 $contact->email1 = $email;
 $contact->created_by = 1;
 $contact->save();

 //Create Opp
 $opp = BeanFactory::newBean('Opportunities');
 $opp->customer_salutation_c = $title;
 $opp->customer_first_name_c = $firstName;
 $opp->customer_last_name_c = $lastName;
 $opp->name = "$firstName $lastName"; //This matches formula on leads
 $opp->customer_full_name_c = "$firstName $lastName"; //This matches formula on leads
 $opp->gender_c = $gender;
 $opp->date_of_birth_c = $dateOfBirth;
 $opp->age_c = $age;
 $opp->primary_address_street_c = $street;
 $opp->primary_address_city_c = $town;
 $opp->primary_address_state_c = $county;
 $opp->primary_address_postalcode_c = $postCode;
 $opp->phone_home_c = $phone;
 $opp->phone_mobile_c = $mobile;
 $opp->email1 = $email;
 $opp->created_by = 1;
 $opp->save();

 //Create Lead
 $lead = BeanFactory::newBean('Leads');
 $lead->customer_salutation_c = $title;
 $lead->customer_first_name_c = $firstName;
 $lead->customer_last_name_c = $lastName;
 $lead->first_name = $firstName;
 $lead->last_name = $lastName;
 $lead->name = "$firstName $lastName"; //This matches formula on leads
 $lead->gender_c = $gender;
 $lead->date_of_birth_c = $dateOfBirth;
 $lead->age_c = $age;
 $lead->primary_address_street = $street;
 $lead->primary_address_city = $town;
 $lead->primary_address_state = $county;
 $lead->primary_address_postalcode = $postCode;
 $lead->phone_home = $phone;
 $lead->phone_mobile = $mobile;
 $lead->email1 = $email;
 //Non fields
 $lead->status = 'Converted';
 $lead->converted = 1;
 $lead->contact_id = $contact->id;
 $lead->account_id = $account->id;
 $lead->team_id = 1;
 $lead->team_set_id = 1;
 $lead->created_by = 1;
 $lead->save();
 
 //Process relationships
 $contact->load_relationship('leads');
 $contact->leads->add($lead->id);
 
 $account->load_relationship('contacts');
 $account->contacts->add($contact->id);
 
 $opp->load_relationship('accounts');
 $opp->accounts->add($account->id);
 
 $contact->save();
 $account->save();
 $opp->save(); 
 
 Thanks!

Calculated Fields not updating on $bean->save()