Yup, I just wasted several hours due to this same problem.
When an App Store version of your app is installed on your device, and you try and install an Ad-Hoc version on top (even with a later version number), then the device just ignores it. Nothing gets installed, nothing appears on the screen, but it quietly logs that message.
<Warning>: ExternalDownloadManifest: Skipping download and install of: com.purplecover.anylist
Why would you not display an error message, when your device has decided to ignore such an install ?
This really is Apple at its very worst.
I wasted further hours due to my Provisioning Profiles being marked as "Invalid (managed in Xcode)". The solution was to delete our perfectly valid "iOS Distribution" certificates and recreate them. And yet more hours trying to get around misleading In-House install errors which were actually caused by the
"Apple Worldwide Developer Relations Certification Authority" having expired. Once again, Apple knew about this issue, and made no effort to help developers who got stuck by it. No useful error messages appear, you're just expected to burn hours, Google what little messages you can find in the log, and hopefully stumble across the problem that their expired certificate has caused.
Imagine if us develoers decided to follow Apple's example.
"Ahhh, my iPad app can't contact its web service. Let's just silently add a log entry which the user won't be able to see, show nothing on the screen, and leave the user to wonder what's just happened."
If an error has occured, report it to the user. It's common sense.
Oh, and another one I've hit today.
Our company has an iPad app in the App Store, but strangely, the App ID identifier had disappeared in the "Certificates, Identifiers and Profiles" screen, so I can't build a new version using this same App ID. If I try to create a new App ID with this ID, I get an error of "An App ID with Identifier 'com.mycompany.myappname' is not available. Please enter a different string."
Once again, this is Apple's error handling at its worse. Actually, what the problem is is that Apple has changed its rules. Now, the app ID *must* be com.mycompany.myappname.somethingelse. Does the error message give any hint that this is what's causing the problem ? Of course not. Once again, you're left baffled as to what Apple has broken/changed this time, and left Googling to fiind other victims with the same issue.
I hate Xcode. Every year. Every release.
It just keeps getting worse.