Cocoapods Warning – CocoaPods did not set the base configuration of your project because because your project already has a custom config set

I had the same problem, but in Xcode 6.1.1 – what fixed it for me was to change the configuration file setting to None for the two Pods-related targets, then run pod install again.

The configuration file setting is found by selecting the project (not the target) and then the Info tab.