I realize that there are other ways to handle profile relocation for these apps, but my question is more about junctions in general: aren't they supposed to be transparent?
I used Windows 7's Mklink command, and later Link Shell Extension once I learned of it, to create a series of directory junctions for various purposes. Two of which, I noticed recently, were overridden.
First, when running Chrome one day, I noticed that I had a new profile. Looking at the profile dir, I saw that my junction was replaced with an actual dir (appdata\local\google), thus the new profile. I deleted it and recreated the junction, and it's been fine since.
Another day, I noticed the same thing happening with Firefox (in this case, appdata\roaming\mozilla -- the one in local was fine).
I suspect the updaters for both apps were behind it, but it certainly doesn't happen every time they're updated.
Windows 7 x64 SP1