Just to tidy up the thread..

1. I adjusted the default tool for the the installer and made sure it is the supplied installer that comes with Pagestream. By default the MOS installer was running and installing Pagestream

2. I followed the suggestion of pointing the Default Font Drawer to Pagestream:Fonts and created a "Truetype" folder in the default font drawer for new fonts.

3. I also emptied the CSets folder and moved everything to 'Disabled'

Thanks again, just posting here what I did in case someone needs it for future reference.