I noticed this happening with R source code blocks after the upgrade. The simple example is below. The resulting html file has different time in the "Time" section than the org file. Reverting to 8.3.6 fixes the issue.

Thanks,

Alex

* Environment

#+begin_src emacs-lisp :exports both :results output

(prin1 org-export-babel-evaluate)

#+end_src

#+RESULTS:

: nil

#+begin_src emacs-lisp :exports both :results output

(prin1 (org-version))

#+end_src

#+RESULTS:

: "9.0.1"

* Time

#+begin_src R :session *R* :exports both :results value

Sys.time()

#+end_src

#+RESULTS:

: 2016-12-01 16:52:43