You've got that backwards.

The stay itself only posts 600 "miles".

It's the MegaMiles bonus that posts the additional 1200 "miles".

So if you were getting a check-in bonus, it would have to be yet another 600 "miles", for a total of 2400 "miles" per stay.

So it looks like you're not getting a check-in bonus, you're simply mistaking your normal 600 "miles" earning for a check-in bonus when it's actually your normal stay eraning.

Go back and see what you earned on your first stay under this MegaMiles (the first stay didn't earn the 2x, it only qualified you for earning that on subsequent stays). I bet it was 600 only, not 600 + 600.