I was facing same issue, resolved using command line "xcodebuild" tool script, which is preinstalled with Xcode 6 (didn't need to re-install Xcode 5).
http://www.thecave.com/2014/09/16/using-xcodebuild-to-export-a-ipa-from-an-archive/
Script in terminal:
xcodebuild -exportArchive -archivePath $projectname.xcarchive -exportPath $projectname -exportFormat ipa -exportProvisioningProfile 'Provisioning Profile Name'
I had a similar issue when submitting to The App Store. I created an archive, then clicked "submit" and Xcode wanted to automatically sign with the default "XC com.*" wildcard provisioning profile instead of the explicit profile that already had.
To fix this, I just re-generated the profile on the Apple Developer Portal:
1) Go to developer.apple.com and find the distribution provisioning profile you want to use.
2) Select it, click "Edit", re-name the profile, and click "Generate".
3) Download the provisioning profile to the Desktop and drag it onto the Xcode 6 icon.
4) Re-start Xcode 6.
5) Open the organizer window and click "Submit" on the archive you built. Xcode will automatically pick your explicit profile instead of the generic one.
Once you are in Organizer
Of course you need to have generated, downloaded and installed the ad-hoc provisioning profile.
It seems the last generated provisioning profile wins right now. So you can just re-generate the profile you want and download it and Xcode will use it.
A slightly better approach: set the desired prov profile in your target and use the command line to build your ipa, that works, too.
Here is the script, I'm using:
#!/bin/sh
# Current as working as of 2014/09/22
# Xcode 6
OUTPUTDIR="$HOME/build"
APPNAME="your-app"
SCHEME="your-app"
APP_WORKSPACE="$HOME/Path/To/your-app.xcworkspace"
rm "$OUTPUTDIR/$APPNAME.ipa" #deletes previous ipa
xcodebuild -workspace "$APP_WORKSPACE" -scheme "$SCHEME" archive -archivePath "$OUTPUTDIR/$APPNAME.xcarchive"
xcodebuild -exportArchive -exportFormat ipa -archivePath "$OUTPUTDIR/$APPNAME.xcarchive" -exportPath "$OUTPUTDIR/$APPNAME.ipa"
and my settings:
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