I've just uploaded my first app to Android Market. Strangely, there are some major differences between the pkg I installed directly on my phone and the pkg I downloaded from the Market after I uploaded.
How odd! What is going on? All these things worked fine in the pkg that I put on my phone without passing through the market.
One explanation might be that somehow the market mixed up the old pkg (which I deleted) with the new. This is unlikely, since the app walks and talks like the most recent version and not like that old test version. Also, the manifest contains new permission requests that weren't in the old test version.
Another suspect is the (deprecated) copy protection in Android Market. I'm trying to get rid of that now and see if it helps any. But why it would mess with details of the manifest or block jsonp I don't know.
The app is located here for anyone wanting to test (it's free): https://market.android.com/details?id=com.phonegap.affordit (As of yet there are no downloads except by me, since I postponed marketing until I was sure it would really work. Glad I did that!)
I've never seen this, though I am aware that new APKs you upload can take a while to show for download. I'd certainly make sure the APK you're downloading is the version you think it is, not the previous one.
It seems highly unlikely the Market would mess with APKs in this way. I expect it's a simple case of mistaken identity.