The second smaller GPX contains any addition public waypoints added by the geocache owners of the geocaches your PQ included. The current GSAK doesn't really know how to handle them. If you have GSAK process this smaller GPX it will basically add them as if they are geocaches but with lot of the information missing since they aren't really geocaches.

On Clyde's support board http://www.gsak.net/board/ he is asking people what they want done with them, before he started updating GSAK.

Thanks, Allen.

I think he is at minumum planning to some how link the extra waypoints to the correct geocache.

But in the mean time has a update so that you can tell GSAK to ignore the extra waypoints until he can update GSAK to handle them in a logical manner.

Read about it here http://www.gsak.net/board/index.php?showtopic=961&st=0&#entry6685 and go down to the lastest build if you want to be able to tell GSAK to ignore the extra waypoints.