Perhaps you are using gfortran older than 4.3? Please update your gfortran compiler.
Certain versions of the Intel Fortran compiler implement “dummy reads” in a very stupid way. This makes seeking very slow in large files, which can affect calculations on large molecules. The issue is reported to Intel, but affect ifort at least up to version 10. As far as we know there is no solution except to use a different compiler.
All libraries have bugs and we have experienced one in an older MKL library (http://software.intel.com/en-us/forums/intel-math-kernel-library/topic/61244/). In doubt update MKL or use the built-in LAPACK implementation.