Hi, I haven't experienced this problem. Are you aware that things have changed in the last month or so in regards to punch cards? Namely, that if you use a coupon code to purchase a game, you will only receive a punch on your punch card for that game if you use it during a bonus punch promotion (which currently takes place on Mondays).
I don't know if this accounts for the discrepancy you are seeing on your punch card, but I thought I should mention this, just in case.
Quote from the Big Fish website:
Due to recent changes in the Game Club Punch Card program, redeeming a Punch Card coupon code for a free game will no longer earn a punch on your punch card. You can still get a bonus punch for using your Punch Card coupon code during a Bonus Punch promotion.