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Reading carefully the output, looks like you compiled and installed gazebo using a previous version of protobuf (probably 2.3). Now you have a newer version (2.4) and the previous compiled code using 2.3 can not work with current installed version.

I would try to compile gazebo with the new 2.4 protobuf library and install it again. If re-compiling is not an option, yes, downgrade the protobuf libraries should work.

I compile gazebo everyday against 2.4.1 protobuf library and it is perfectly compatible.