I appreciate it's been a few days since a reply..
Just to clarify things.
The encroachment was as much as he was in line with the penalty taker on both occasions, having effectively got in between me and the kicker/penalty mark on the actual kicking off the ball. This is no 1 or 2 yards which I generally accept unless it is a clear advantage to the defending team.
My positioning etc during a penalty is as follows:
Talk to the player first and foremost once the ball has been placed and I am happy that he must wait on my whistle.
Talk to the keeper, asking that he remains on the goal line until the kick is taken - not too fussed if a yard off when taken as for me it's natural movement.
Talk (loud enough for all to hear whilst looking at all in a general sweep) to all players on the edge of the area/D that they should not be in until the kick is taken - and like the keeper, not generally fussed over a yard or so.
The fact this player was already in the forefront of my mind following his dissent he'd just dished out, he came in a good 6 or 7 yards to be a couple of yards from the kicker upon the actual kick of the ball. Keeper saved it and on this I awarded a retake.
I normally watch the kicker at first with one eye on the outside and sweep in towards the kicker and keeper on the kick off the ball to ensure the keeper is on, or at most a yard off, the line. Penalise if need be. I also stand between the 6 goal area and penalty mark (away from goal obviously) so that I have a wide view of the set piece.
So once the first penalty was taken, and saved, I blew whistle and called captain and offending player in. This was more not to give a rollicking to the offender but to remind him that he must stay out the area and captain only because he was the only civil person I could explain and be accepted decision.
The chat with them explained why I am retaking and then reiterated my initial words to those outside the area that they must remain outside the area until the ball is kicked.
Ball placed down and same process again, tell kicker on whistle, keeper to stay on the line and players all out of area and said sterner this time, a little more aimed at the player late given 2nd caution.
Blew whistle and the defender is again in line of the kicker at the point of kicking the ball.
Ball saved again by the keeper and so I resorted to blown whistle again and ordering retake.
Having just had a word with him for it, making it 3 times he heard it (first sweep before 1st penalty, his talking to with captain and the 2nd sweep before 2nd penalty) I felt he was ignoring me and decided to caution him for persistent infringement. The fact he had a caution moments earlier had no effect on this caution other than it lead to being a red.
I felt that if I didn't act on it then people will ignore my warnings later on.
This was my thinking/logic around all this.
Hope it explains it a bit more and those can understand it from my perspective.