This is primarily a programming language issue:

The data itself in HDF5 is exactly the same. HDF-Java reads the data in row-major order. If your data was written with a Fortran application, then the data will appear to be transposed in HDFView.

Since HDFView does not know how the file was created, it provides a way to swap the dimensions if need be. You can change the order that the data is read and viewed as follows: