Upline / Downline Tracking

I created an affiliate system following the documentation to the letter. At the end I had a system that could accurately track clicks from affiliate links but I am having issues with the tracking of the uplines and downlines.

I created an account for Joseph and went to another computer to use Joseph's affiliate link to refer Raphael. Now I have authenticated users on the site and then a role called 'affiliate' to which authenticated users apply to join as affiliates [i told u i followed d documentation]. Now when i created Raphael's account and I had not applied for Raphael to be an affiliate, I checked Joseph's affiliate center and found that Raphael did not appear in his downline. Now I went and made Raphael and affiliate and yet on Joseph's account, Raphael does not still show as a downline referral.

Only strangely that on Raphael's own affiliate center, himself appears as his own downline but Joseph does not still appear as his upline.

The core things I need on my site is to track clicks on affiliate links and to track their referrals. I want the referrals to track as they register on the site regardless of whether they join as affiliates or not.

Thanks if you could help.