The normal cause of this is that your #2 kicker is #1 on the depth chart elsewhere (usually you have the #1 FG kicker = #2 Kickoffs and vice versa, or you have your #1 punter in as #2 on kicks, etc). What happens is the #1 FG kicker gets benched when starters are pulled, and the #1 Kickoff player also gets benched - because they are both benched, neither are available to enter the game at the other position. Basically, the starters are only benched if there is a #2 behind them, but if the #2 is also a #1 elsewhere the depth chart ends up getting emptied and it falls back on the best player available (which for a kicker is pretty much randomly whoever has the best kicking attributes)

Ah, ok. Yup I did that. My bad, sorry. Thanks!

Yes, make sure your kicker and punter are unchecked in the box where you indicate which starters should be pulled.

Check to see if you have 1 kicker #1 for kickoffs and the other kicker #1 for field goal kicker. If this is true, I believe it is because in the pre-season starters are taken out after 1,2,... quarters. Technically, if they are both starters, neither will play when starters are taken out, hence the position players will do the kicking.

EDIT - Okay, I only saw page 1 before posting. And I see JDB has answered this! Carry on...