Is there a way to set the keeper rules so that players not drafted by a team can not be kept as keepers this season? I have a few times that snatched up IR players near the end of the season and are now set as keepers.
I looked through keeper rules, but that only allows me to set how many keepers each team can have.
IF I can't change that, what draft pick do these FA pickups cost those teams?
You would have to manually edit their rosters and have them removed there at League>>Settings>>Edit Rosters -- there is nothing automatically in place to prevent non-drafted players from being picked up and kept.
Fleaflicker defaults all keepers that are kept to that team losing a pick at the end of the draft regardless of where they're drafted. You can edit keeper spots on your own by editing the draft order if you want a player to take up a certain spot. You can read about that here (it's towards the bottom):