As far as I'm aware, the latest version of shifter works with release1 of HDTP, not the beta. Shifter is coded to work entirely separately from HDTP: it doesn't use any HDTP code directly, instead simply looking for HDTP assets (models, textures) and then using them appropriately.

So do you actually make new ini files and create a shortcut to HDTP? Because that's one of the things the installer does, and it's pretty vital to actually using the HDTP assets.