Here is my html with a php script:
Bob\'s Auto Parts
Make sure that you are using and not shorthand since that may be disabled on your server. This will cause the output of "; ?> as it happened to me a few months ago in a transition to PHP5.
I've only seen the odd output like this when the PHP parser isn't detecting it as PHP. Make sure to check that PHP is functioning as expected and that the tag is being recognized.