I' having the same issue with a new app I'm trying to upload today. But here are my inputs:
1 - I have a family suite of apps (about 48) called "You Know You Are" (ie: You know You Are a Guy, You Know You Are from Miami, etc). Each have their own unique appID. Out of those 48 only ONE of those appear in ENABLE iAD section.
2 - I have another set of app call "How Long Can You" (ie: How Long Can You Tap It and How Long Can You Turn It). I never created a unique appID for these. The app bundle DOES have each of them unique(com.site.tapit, com.site.turnit) and the Distribution profile I sign it with with the wildcard profile. When I went to update those apps yesterday, they DID show up. No typo here, I double checked, YES I did say that I WAS able to enable iAd for those two apps.
I was reading a bit on why only one my other family apps appear in the list. I came across this thread and decided to add my 2-cents, more like 1-and-a-half-cents since I feel none of this makes sense ;)
Also, I decided to follow instructions and I just added a new AppID for a new app I want to upload and I still do not see it in the list.
Hope this sheds some light to help fix/diagnose what is going on.