First of all, you're using wrong path to --with-jpeg-dir. It expects /usr without the "/lib" part which in your case is most likely not lib but lib64 anyway. 

But I can not reproduce this using proper sources downloaded from php.net. Did you by any chance do buildconf or autoconf yourself?

I don't use any path in my example. That was not my URL but some other guy. No, I did not any custom configurations. Did you try 5.3.3?

5.3.3 works just fine for me regardless of the order of those parameters. Only difference in my test was the use of '--with-libdir=lib64' since I only have 64bit libs around. So you're not telling everything, for starters, what was the FULL configure line you tried which failed?

Hello. 

Full configure line is as follows:

./configure --enable-bcmath --enable-calendar --enable-calendar --enable-exif --enable-exif --enable-fpm --enable-ftp --enable-ftp --enable-gd-native-ttf --enable-libxml --enable-magic-quotes --enable-mbstring --enable-mbstring --enable-pdo --enable-soap --enable-sockets --enable-wddx --enable-zend-multibyte --enable-zip --with-bz2 --with-bz2 --with-curl --with-curl --with-curlwrappers --with-gd --with-jpeg-dir --with-png-dir --with-libdir=lib64 --with-mcrypt --with-mysql=mysqlnd --with-mysqli=mysqlnd --with-openssl-dir=/usr --with-openssl=/usr --with-pdo-mysql=mysqlnd --with-pdo-sqlite --with-pear --with-pic --with-sqlite --with-tidy --with-xmlrpc --with-xsl --with-zlib --with-zlib

Before executing it I've also done:
yum install autoconf libtool httpd-devel libxml2 zlib-devel libxml2-devel openssl-devel bzip2-devel libpng-devel libtidy-devel libxslt-devel libevent-devel curl-devel libmcrypt-devel libtool-libs libtool-ltdl-devel

Why did you need to install autoconf? Are you still claiming you did NOT regenerate configure at any point? What does it say in configure about the version? (search for "autoconf version" :)

I can not reproduce this with the configure generated the only working autoconf which is version 2.13. If you have regenerated configure, the support ends there.

I'm installing autoconf because I need it to build whatever. For example, PHP extensions. I did not regenerate configure.

The autoconf my systems use is the CentOS standard one:
autoconf.noarch                        2.59-12

It is not 2.13.

Well, it does work for me fine whatever the order of the options are.

I'm sorry for a stupid question, but did you do "make clean" between tests?