I searched and found out how to run behat as an exteranl tool and it will work with the project as long as I throw exceptions and don't try to use PHPUnit asserts.
After considerable searching I have discovered the problem.
I am using a MacBook Pro running the lastest OS X and updates. I am using PHP 5.4.10 from the MAMP distribution for the project as installed from the DMG distribution. OS X comes with a default PHP installation installed in /usr/bin. In PhpStorm, I have set up installed the PHP version and I can build and run my project without problems. It is only when running behat as an external tool that I run into problems.
The difficulty is that PhpStorm places /usr/bin at the front of the PATH variable when running an external tool or running command line. The result is that when behat runs, it sets the php default library to /usr/lib and not to the version of PHP that I have set for the project. PHPUnit and a number of other utilities / extensions are all installed against the PHP 5.4.10 MAMP installation that is in the /Applications/MAMP/bin/php/php5.4.10/bin and lib directory. The result is that behat / PHP can't find the PHPUnit code that it requires. If I specifically put the absolute directory location of PHPUnit in the requires_once then it fails in PHPUnit because it is assuming that it is in the library path or a specific location relative to the project.
To confirm my suspicions, I used the terminal (command line) and made sure the PHP path was set to my desired version of PHP. Going to the base project directory and running behat shows that all the tests pass even using PHPUnit asserts.
NOTE: My setup is assuming that all my utilities are gloabl to the project and have been installed outside the project using composser. I haven't tried using composer withint the project to install PHPUnit, behat, and mink as project specific but since this is linked with the running of a PHP version, I suspect that some of the same problems will occur.
Have others experienced this problem when using different versions of PHP in PHPStorm.