First, i have some older files from PHP since back in the day that are .phtml files. Joe doesn't recognize these as PHP.
Second, compared to "vim", the color coding in Joe is really lacking for PHP files. Many of the key words are missing and it just doesn't seem to be as comprehensive.
And the color coding syntax for .rb (ruby) files is even worse. It amounts to green comments, white begin/end, teal for strings and everything else is gray.
This is a radical idea, but couldn't you change your parser engine to use whatever Vim uses? Then you could get the benefit of their color templates and all that magic but with the ease and convenience of Joe's editor.