Whoever provided the copy of HEC-GeoHMS to you should have provided the ApFramework and Arc Hydro tools (prerequisites for GeoHMS). If you got it from HEC's web site, that version contains full installation package, so this problem should not appear. It is hard to diagnose the installation problems without more detail on the source of the GeoHMS package. The 9.3 version has not been updated in a while, so I am not sure what the reference to "new version" relates to. The safest way is to uninstall HEC-GeoHMS, Arc Hydro, and ApFramework you have currently installed (and preferably clean the registry), download the official HEC-GeoHMS from HEC's web site, and try to install it again.
Dean