As sXi pointed out, the first php binary found in PATH is that of php-cli 4.4.9
When you built PHP 5.2.9 you should have two binaries - the CGI version and the CLI version. Running a binary with the -v argument will tell you what version it is. You need to determine the absolute path (/home/username/[build_dir]/bin/php ) and make note of it.
Then your commands for the cron job need to specifiy the location of your PHP.ini as well as the php-cli binary, something like
/home/username/[build_dir]/bin/php -c /home/username/PHP.ini -f /home/username/script.php
You might want to try running similar command from shell first to test it out:
/home/username/[build_dir]/bin/php -c /home/username/php.ini -v
/home/username/[build_dir]/bin/php [continue] -c /home/username/php.ini -r 'phpinfo();' | more
Edit: changed paths for literal interpretation to avoid confusion.
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