Did you put punters in your manual draft list? Here's how the algorithm works:
When your pick goes on the clock, if you have a player in your manual list, that player will be selected. Other players in your manual list will NEVER be automatically removed unless they are drafted by you or another team. So if you stack your manual list with punters and are not around for 4 picks, those 4 picks will pull punters from your list until they are all gone.
If you are not going to be able to update your manual list then you should adjust your auto-list to give you what you want. The auto-list WILL take into account the number of players who have been drafted at the given position. The way the auto-list works is that each player receives a grade; the grade is calculated somewhat as follows:
1) The base rating value of the player (halfway between current and future according to your weights)
2) Multiply that value by the weight in your draft preferences.
3) The number of players you wish to draft at that position is calculated. This is just the number you have for the goal minus the number of players you have already drafted at that position.
4) If the value from #3 is less than zero, the weight is halved that many times (so if the number is -2, it will be multiplied by 0.25). If it is greater than zero, the weight is increased (not linearly and not as extremely as the other direction).
The only way you should have drafted multiple punters would be if your manual list had them or your weights were such that even with the drafted punters they still came out more heavily weighted.
Hope this helps -