As I mentioned in this stackoverflow thread:
There appears to be an issue with Cordova's iOS implementation when publishing apps created specifically using Xcode 7.
A Cordova community member has published a "cordova-plugin-ipad-multitasking" plugin with a fix.
http://npmjs.com/package/cordova-plugin-ipad-multitasking
Install this plugin and you should be all set. A future Cordova version will resolve the problem fully.
Failing that, if you are using remotebuild you can also find the native project under ~/.taco_home/remote-builds/taco-remote/builds and make the modifications as described in the Cordova bug on the issue.
EDIT:
To resolve ITMS-90339, there is a second step you can do to patch in the near term. Grab the build.xcconfig from the 3.9.x branch of the cordova-ios repo and place this under res/native/ios/cordova
Now remove this line:
CODE_SIGN_RESOURCE_RULES_PATH = $(SDKROOT)/ResourceRules.plist
Note that you will want to remove this custom build.xcconfig file if you upgrade to the version with the full patch that is forthcoming.