Depends on what prizes are being assigned, if they are for splits and even if your league has splits. You also need to be at the end of the split/season when you assign those prizes.
1) If you have Individual Prizes assigned for "Anyone" then these will not be assigned. We are working on correcting this.
2) You can't assign Season awards unless you set the Team Standings to be based on the "Entire Season." This needs to be set even if you don't have any splits in league. You set this in the Rules on the Split Season tab.
3) If you have Awards for each Split, then these need to be awarded in the week for the end of that split. Note here, to assign Split Awards, you need to set the Team Standings to be based on the "Current Split."
Assuming that you have the setting correct for the Prizes you wish to award, you may still need to make adjustments as the Automatic Prize Assigning does not take into account ties.