I have never have this problem before but spoke to a friend and they are having the same problem.
Occasionally (I would say once every hundred hands or so) one hand will not import into pokertracker. The hands always seem to be hands with large pots (possibly ones where there was an all in and a call, friend confirmed this as well - but we are unsure.) All we know for certain is this is only happening since the most recent update to 4.15.37 on October 19th.
Edit: I can't seem to find on the website a link to past versions, if someone could direct me to the previous version that would be great as I would like to revert for now since this problem was absent in the last version.