Newbie knitter ideas:
Did you possibly leave a different number of stitches at the turn on each end of the heel? Or maybe you did like I did once, and neglected to actually turn the heel. I just picked up the gusset stitches and went on my merry way--my first serious frogging...
If it's an inconsistency problem, the only cure is practice. If the stitches are obviously looser, I'm kind of betting that's not the issue. There aren't all that many stitches in a heel flap, so a slight variation in size wouldn't make a humongous difference.
I'm sure a more seasoned knitter may have more insight.