HI!
I installed Anaconda on a windows server, for all users, then I followed the set-up in my workspace TOOLS > "FME Options" > Translation > "Python Interpreter" checked "Use Custom Python Interpreter" and provided the path (C:\ProgramData\Anaconda3\python36.dll)
The log then shows :
Loaded module 'PythonFactory' from file 'C:\Program Files\FME2016\plugins/PythonFactory.dll' FME API version of module 'PythonFactory' matches current internal version (3.8 20160224) The user-specified Python interpreter `C:\ProgramData\Anaconda3\python36.dll' is version 3.6 (PythonFactory): A Python installation could not be detected. PythonFactory could not initialize A Python installation could not be detected. PythonFactory could not initialize A fatal error has occurred. Check the logfile above for details