I just wanted to add below in addition to the verified answer for a very specific scenario.
Recently, I was asked to fix the same problem that OP was experiencing for a work computer in which user accounts were recently included in the new domain.
Setup: Visual Studio 2013 PTVS 2.2.30718 Anaconda 3.5
Basically, Anaconda was installed for localmachine / UserA.
Once users were transferred to the new domain (newdomain / UserA), the Python environment needed to be updated from VS2013 by clicking View> Other Windows> Python Environment.
Once this has been installed, python scripts will work as expected, although none of the links in the search folder will work. Then they were deleted and re-added, but to no avail.
Various other things were tested, including creating completely new projects and linking them using search paths, but to no avail.
The only thing that fixed the problem was to reinstall the Python environment (in my case Anaconda3) outside of the user account (by clicking the "for all users using administrator rights" button during installation).
Then I restarted, deleted and added the search folders again, and python worked as expected, including all the search paths.
I hope this helps someone as I just spent a lot of time solving it ...
D :)
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