With this being a SSI, you probably don't want to even call the start_html method. That is going to print new <html>, <body>, and <head> tags, which the main page most likely already has.
The HTML page also probably already includes the style sheets. What you need in your perl script is some HTML that uses the classes in the already existing style sheets. What's confusing is that the .inc file worked correctly and your perl script isn't. What's the difference between the two?
Also, if you can post a minimal example of what the HTML page and the perl script are doing, that might be helpful.
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