By Default .php is one of the banned extensions for the File Manager.
to change this, go to the webassist/kfm/initialize.php and edit the following line:
$kfm->defaultSetting('banned_extensions',array('asp','cfm','cgi','php','php3','php4','php5','phtm','pl','sh','shtm','shtml'));
to remove php from the list of banned extensions and allow the file manager to link to php files.