The search engines use the html output that your php code generates, so, no, the source being php doesn't affect your search results.
There are many more factors which will be affecting the site search results.
Meeting the W3C standards for the code,
SEO friendly URL's,
good original content,
Searchword competition,
your site's age on the Inter-webs
are a few of the ones I can think of off the top of my head.