Steve Dower added the comment:

Looking at those logs, it seems like we think the per-user packages are already 
installed. When you go to do an all-users install, it "removes" the per-user 
packages, but passes in the same options as it does for the all user packages.

Under the hood, these packages are actually identical, and we run them with 
different options depending on what sort of install you're doing. One of these 
options is the install directory. When we install the all users package to 
C:\Program Files, then remove the per user package from C:\Program Files, it's 
actually just removing itself immediately.

I *think* the best way to deal with this, given that running the msiexec 
commands didn't work, is to do a Just for Me install first, and then uninstall 
that and do the All Users install.

---

You can see in the main log file lines like this:

[1B20:05AC][2016-11-28T11:44:53]i301: Applying execute package: core_AllUsers, 
action: Install, path: C:\ProgramData\Package 
Cache\{EB0611B2-7F10-4D97-BCF2-DCAAB1199498}v3.5.2150.0\core.msi, arguments: ' 
ALLUSERS="1" ARPSYSTEMCOMPONENT="1" MSIFASTINSTALL="7" TARGETDIR="C:\Program 
Files\Python35-32\" 
OPTIONALFEATURESREGISTRYKEY="Software\Python\PythonCore\3.5-32\InstalledFeatures"'
[1064:274C][2016-11-28T11:44:59]i319: Applied execute package: core_AllUsers, 
result: 0x0, restart: None
[1064:274C][2016-11-28T11:44:59]i329: Removed package dependency provider: 
{EB0611B2-7F10-4D97-BCF2-DCAAB1199498}, package: core_JustForMe
[1064:274C][2016-11-28T11:44:59]i301: Applying execute package: core_JustForMe, 
action: Uninstall, path: (null), arguments: ' ARPSYSTEMCOMPONENT="1" 
MSIFASTINSTALL="7" TARGETDIR="C:\Program Files\Python35-32\" 
OPTIONALFEATURESREGISTRYKEY="Software\Python\PythonCore\3.5-32\InstalledFeatures"'
[1064:274C][2016-11-28T11:44:59]i319: Applied execute package: core_JustForMe, 
result: 0x0, restart: None

Notice that the package names (core_AllUsers, core_JustForMe) are different, 
but TARGETDIR is the same. It also seems that the packages are always ordered 
all users first - possibly this issue could be avoided if we did not interleave 
the packages, though you'd likely still not get a working install at the end.

----------

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Python tracker <rep...@bugs.python.org>
<http://bugs.python.org/issue28781>
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