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Perhaps if you explain why you think your php pages are having a negative ranking effect someone here may be able to advise you further.
Am I better to include keywords in my .php files too then? Will they get read?
PHP runs on the server to generate the html code, and you have complete control of the html in exactly the same way as when you write a static html page in your editor.
The only potential problem I can think of is where php is set to append a sessionid onto the end of your urls. If you're not doing this, spiders/search engines will have no problems indexing your php pages.