In "The Power of Three", Amy & Rory talked about the mismatch between how much time they'd lived through & the calendar dates of various celebrations. They were holding those celebrations on the dates expected by their friends & families (who, except for Rory's father, didn't know anything about their time travelling). In effect, this meant that Amy's birthday hadn't changed -- it was just that it no longer had very much to do with Amy's age. "The Girl Who Waited" was only one of many adventures that contributed to the mismatch between the date & Amy's age.
This mismatch, for both Amy & Rory, became far more drastic (& inexplicable to others) after they were sent back in time by the Weeping Angel at the end of "The Angels Take Manhattan" & lived out most of their lives before they had been born.