Sounds like issue 454
  https://github.com/rordenlab/dcm2niix/issues/454

This will be resolved in the imminent next stable release. I believe using LLVM or a more recent version of GCC also resolves this. The easiest way to resolve this by compiling the development branch:

git clone --branch development https://github.com/rordenlab/dcm2niix.gi...
cd dcm2niix/console
make
./dcm2niix

I feel confident this will resolve your issue. If not, please tell me.