In this case we recommend to check what tracking code you have in the signup page source code.
Most of older Post affiliate pro releases have/had this one:
<script id="pap_x2s6df8d" src="../scripts/trackjs.php" type="text/javascript"> </script>
<script type="text/javascript"> papTrack(); </script>
Problem was that from time to time such code did not register a parent ID (referred affiliate ID)
So our developers made a quickfix and the newer versions of post affiliate pro have this code in their signup pages
<script id="pap_x2s6df8d" src="../scripts/trackjs.php" type="text/javascript">
</script>
<script type="text/javascript">
papTrack();
PostAffTracker.writeCookieToCustomField("visitorId");
</script>
Do you see that additional line in there?
This one:
PostAffTracker.writeCookieToCustomField("visitorId");
So in case your affiliate signup under a parent affiliate doesn't work due to any unknown reason.. please check the tracking script in your signup page
and if the additional line is missing there.. simply modify the signup page theme.. search for footer.stpl template and add the mentioned line into the tracking script.