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I can't reproduce this issue by following the steps in your report.

To move forward:

• provide reproduction steps which work in a clean environment; or
• we'll close this report in a few days if we don't receive the information we need.

That's the big problem, the logs say nothing.

To libphutil and arcanist I put them in the php include_path.
Arcanist 3b6b523c2b236e3724a1e115f126cb6fd05fa128 (18 Feb 2017)
Libphutil 13a200ca7621ab2b48a0c395f52f8c4411bbc686 (Mar 4, 2017)

This is where I can tell you, the httpd logs, I repeat does not say anything about a bug related to phabricator.

Did you try to enable PHP's error logging to get more output?

See also PHP's documentation