h3. Behavior: Zend_Application_Bootstrap_BootstrapAbstract::setOptions() merges given options but not its keys.

h3. Effect: If options are set multiple times, only keys of the last options-set are registered. Later calls of Zend_Application_Bootstrap_BootstrapAbstract::hasOption() will fail for overwritten keys.

 
public function setOptions(array $options)
    {
        $this->_options = $this->mergeOptions($this->_options, $options);

        $options = array_change_key_case($options, CASE_LOWER);
        $this->_optionKeys = array_keys($options);
        ....

h3. Suggested solution: Replace

 $this->_optionKeys = array_keys($options);

with

 $this->_optionKeys = array_merge($this->_optionKeys, array_keys($options));