If I understood Goodall correctly, he told me that they encountered snuffer problems similar to what you're describing until they added a third hole/patch right at the bottom (centered) of the spinnaker. This guides the initial "wad" in. I don't know if this would be relevant with your system, though, since it is an end-pole snuffer.

A photo can be seen at this web site: http://www.taipan.asn.au/
Look under Photos at the Kurnell F16 section--the photo with two blue spinnakers clearly shows the 3 patches.

I'm curious to hear from others about knotting the retrieval line--do most people do this, and if so, at what point above the hole/patches?