>something went wrong with the command, so it doesn't do the
>substitution.  You should have a message along the line "The executed
>custom command returned an error. Your selection was not changed." in
>the status bar.

Those are the first 2 messages (before of "PHP Strict Standards" posted from me):

11:37:07: Passing data and executing custom command: php_beautifier -s4 -l "ArrayNested() NewLines(before=if:switch:while:for:foreach:function:T_CLASS:return:break,after=T_COMMENT) IndentStyles(style=k&r)"
11:37:08: The executed custom command returned an error. Your selection was not changed. Error message: PHP Strict Standards:  Non-static method Console_Getopt::readPHPArgv() should not be called statically in /usr/bin/php_beautifier on line 70