Hey i Had the same problem as well,  I msged the support centre and was given a reply within 6 hours.. Apparently it will not track hits if you have put "Freedom.ws"  in your replicated site. you have to choose any other sites other than "Freedom.ws".

following is the exact message i got from the support team

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Good Morning Brandon,

The Hit Logs will only track  visits, or "hits", to your Affiliate URL
of http://website.ws/username. Your affiliate site is currently
directing to http://freedom.ws/index.dhtml?sponsor=username&chk=1 which
is not tracked in the Hot Logs.

To have your domain successfully tracked please login to your members
area select the "My Replicated Sites" button located on the left and
choose any of the options other then the Freedom.ws capture pages.

If you need additional help, please reply to this email making sure to
include the original messages for an accurate response. If you prefer,
you may call us at (1) 760-602-3000 M-F 8-5 Pacific Time. Please listen
to the entire list of telephone choices in order to ensure you reach the
proper department.

Kindest Regards,

Courtney
.WS Affiliate Support
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Happy GDIng!!