Martin,
I think you are right about this being a HDF5 library version issue. It appears that you originally created a 1.10 compatible HDF5 file because your original Xdmf/HDF5 writer was using a HDF5 1.10.x library version. Then you tried to read the file with ParaView linked with HDF5 1.8.x. 1.8 library versions are not able to read 1.10 compatible files. Superblock 3 is a symptom of 1.10 compatible format.
If you want to keep up with current HDF5 1.10 library versions, there are a couple different strategies. You can upgrade your reader and display tools such as ParaView, to use the current HDF5 1.10.x version. Then your tools will be able to read both 1.8 and 1.10 compatible files.
Alternatively you can use one of the backward compatibility options when creating new files, so that 1.8 compatible files will be written with the 1.10 library. Then you don’t need to upgrade display tools, and your 1.8 files will also work with other people’s down-level software.
Because HDF5 1.10 has now been released for almost three years, I recommend upgrading all your tools to 1.10. Use one of the backward compatibility options when creating files, only if you will be sharing files with other people that might be using down level tools.
Here is more information about backward compatibility options. This is the C API, you might want to look up the equivalent for Java:
https://portal.hdfgroup.org/display/HDF5/H5P_SET_LIBVER_BOUNDS