Update...

Someone at EYW was monitoring this thread, whoever you are thank you! I got an email referring to my previous post and asking me to send in my calculations about the discrepancies. I sent in my receipts showing the time stamp of my booking confirmations and that I should have been eligible for the 2000 wings/segment.

Things aren't quite right still though. I'm now up to 125k wings, however it looks like there was a manual adjustment made which isn't quite right. I've been awarded 72 of the 1k badges instead of 36 of the 2k badges. My wings total is correct however I am still short the 1000 miles that should have been awarded with each of the 2k speed bump badges (36k miles total). The EYW website shows that I've earned 222,000 miles but the total should be 258,000. I think I'll give it a few days to see if the miles post separately before contacting AC yet again.

I'm not sure if other people who had similar issues are going to have miles post, but for now I'm #3!