You need to ditch the egg in both cases. If i'm reading your post right, you save when the girl has an egg. You grab that first egg, hatch it, check IVs, and reset. The next time, you ditch that egg and hatch the next one.
Assuming this is what you did, then yeah it is incredibly likely that you'll get a different IV spread; you're getting the first and second egg of the seeded IV spreads. What you need to do is ditch the first egg, hatch the second, reset, ditch the first egg, hatch the second, and then compare the IVs of both seconds.