On WHMCS, subscriptions can be created (and show on PayFast) but my clients are not able to pay on subscription.

If another payment gateway (such as PayPal) has been used for subscriptions previously this could be a problem and interfere with the subscription token being stored on WHMCS.
Compare the token stored on WHMCS with the token stored on PayFast for the client’s subscription as follows:

1. Go to View Clients > View a specific Client Profile > Go to Products/Services tab. On the right hand side, or the bottom, you will see the ‘Subscription ID’. 
2. On PayFast, when viewing the Ad Hoc Agreements, click the magnifying glass to view the subscription token.
3. If need be, you can replace the token stored on WHMCS with the token stored on PayFast (which is the correct token) in order to allow for future charges.
4. Be careful to ensure that the token is correctly matched with the correct client.