installer.nsi does the bulk of the windows registry work for the new installer. But it currently does all of the browser specific registry keys as well. Rob was talking to me about about moving those out of the shared toolkit .nsi file and into a browser specific file.
This is fixed on the trunk by the patch I checked in for bug 338931
Fixed on MOZILLA_1_8_BRANCH for Firefox 2.0 by the checkin of bug 338931 on 2006-06-13 11:25 PDT