I've run into this problem as well and found a solution that I wanted to share.
You need to have "automatically write changes into xmp" in catalogue settings activated.
You need to have files as DNG (and I did not click "save metadata into file")
I copied the DNG file somewhere else.
I deleted the DNG in LR (and the DNG on my harddisk).
Later I re-imported the DNG file into the catalogue.
The important point is - While Import, in "Apply During Import", do not chose a Develop Setting. Otherwise that will override your settings that are saved in the DNG file.
I now have the DNG file with the development settings that I applied before I deleted the file in the catalogue.
I hope this helps.
For what it's worth, my work can be seen here: http://www.two-in-love.ch