Thanks for the replies.
I now have compression working but I have still to fully test and I am still not really sure what is happening exactly.
It seems that my server is automatically set for mod_deflate, so I dont need to add it in the .htaccess file.
mod_deflate does not seem to compress any file that is output from PHP, no matter what file types I add in .htaccess
I have now added "php_flag zlib.output_compression on" to my .htaccess and this seems to compress all PHP output, with mod_deflate compressing any static content.
Thanks again
Tommy
Update: This did not cure my issues and I ended changing from FastCGI to mod_php and everything works as expected. It appears that the way scripts are handled in FastCGI was causing the issue.