Sorry to say, but the issue in Hugo 0.39: Help test it! - #7 by kaushalmodi is still there (0.40-DEV)… I’ll open an issue for that… Done.
Update: Turns out, this is not a regression… but an issue that I just happened to stumble upon while testing 0.39.1… But it still deserves an issue none-the-less… something to do with baseURL with subdir AND livereload.
Update 2: Sorry for the noise… looks like I got bit by the “fast rendering” this time… --disableFastRender fixed it. I really wonder if that should be made the default… but that’s for another day I guess 
Update 3: So this is a bug with the fast rendering… I wasn’t able to reproduce this issue with a baseURL without a subdir… so something to do with (1) baseURL with subdir, and (2) fast rendering.