I found the same thing (not following my styles as defined in a .clang-format file, which happens to be in the parent directory in my case), and I think that the problem is in the way that the assume-file-name argument is defaulted if absent when calling the function clang-format-region from clang-format.el:
You need to format your numbers with the leading zeros if you want them:
(format "%03d" 3)
When you type
(defvar foo '(00 01 02))
and evaluate it, Emacs reads the string "01" and recognizes it as a
number (integer) and stores it in the list. Then it promptly forgets
how the number was represented - as "1" or "01" or "000001".