When you have multiple installations of PHP, running phpize from a specific installation will not force the module to be compiled with that installation's include files.
In my case, I had a standard PHP distribution installed, and am evaluating Zend Core / Zend Platform, which installed it's own Apache & PHP in a /usr/local/Zend/.. install path. It was missing the json.so module, so I had to compile my own.
Running Zend Core's phpize, the output indicates that configuration for that module will occur. But when running ./configure, the standard installation's include files are used. The result json.so being compiled against the wrong PHP would not load when Zend Core's php initializes.
The only way I could see to correct the situation was to temporarily change the standard PHP include path to point to the Zend Core's include files. In my case, I made a backup copy of /usr/include/php5 and did a "ln -s /usr/local/Zend/Core/include/php/ /usr/include/php5".