If you uninstall stuff that still shows as installed by another emthod then DS will still show it as installed (and will load it if the files are really there).

The only way I can possibly think of for morphs to load onto previously saved items but not new would be if the morphs were in a nested content directory on saving (e.g. My Daz 3D Library/Content/Data/etc. with both Content and My Daz 3D Library set as content directories) - the saved scene might then be including the inner folder in the paths (/content/data/etc.) and if the files were still there they would load, but a newly loaded item would not check the Content sub-directory and so would not see or load the morphs. But that is a fairly arcane set of circumstances.