I recently updated to Xcode 4.6.3 to gain the iOS 6.1 SDK and created a new Cordova project. When it came time to set the Launch Images I encountered weird behaviour; images for certain resolutions were overwriting the images for other resolutions or not updating at all.

When I went to build the project Xcode complained "warning multiple build commands for" XYZ lauch image. To fix this select your build Target then click on the Build Phases tab. Expand Copy Bundle Resources and delete the duplicate entries for your icons and launch images under {Project Name}/Resources/screen and icons/