When installing ACDS 13.0sp1, make sure you change the installation directory in the DS-5 installer to be,
e.g., D:\altera\13.0sp1\embedded\ds-5
otherwise it will be installed somewhere else (probably, but not necessarily, under your 13.0 instalation) and the 13.0sp1 embedded command shell will not be able to find eclipse.
The DS-5 installer will silently delete the old version of DS-5 from 13.0 for you as well.....