If you see massive changes in the configure script after a localized change in configure.ac, it probably means that you're not using the right autoconf version.
Our project convention is to use exactly the GNU release of whichever version of autoconf we're on (currently 2.69). A lot of vendors ship modified-to-some-extent autoconf versions, which can result in these sorts of unwanted changes if you just use whatever is on your operating system. Grab the official release off a GNU mirror and install it somewhere handy, and use that.
As a test case, try running autoconf and autoheader *without* having changed the input files. If the outputs don't match what's in git, then you've got something to fix.