apologies for the slow response.
Add '-D H5_USE_16_API' to the CCFLAGS setting you are using in Makefile.config. This will pull the correct interface, assuming that your HDF5 libs are built with v1.6 compatibility.
The compatibility issues resulting from the interface change for H5Dcreate and a number of other functions is handled via macros, described at this web site:
http://www.hdf.