I have this problem when I try to run my project on Linux (Fedora 20 KDE)
outputKonsole-linux-protobufissue
The first time when I build my app, the compiler didn't find the protobuf, I downloaded the protobuf libraries from github and after installing appears this.
Sorry if my english is not the best and I hope you can help me with this.
As the error message says, your protoc command is a different version from your protobuf libraries. You need to make sure you only have one version of protobuf installed. You should uninstall the version you downloaded from Github (go back to the protobuf code and do sudo make uninstall) and then install the Fedora package instead. This way you can be sure the versions match.
You will also need to clean the cocos2d build directory before rebuilding, to make sure it rebuilds the files using the correct compiler version rather than use the incorrect ones it generated previously.