You are talking about SSI calls. Which deal more with the Webserver rather than perl. If I understand you correctly you are calling an SSI exec directive from another SSI exec directive and you can't do that because the server doesn't parse the included exec or include files. Even if you could its not really a good practice (i.e. you should separate your webpages in very definable sections).

You could use perl to parse out the SSI directives and call the programs or files yourself, but I think it would be far easier to rethink the design a bit so that your SSI calls are all on the page you are viewing.

Hope that helps
Chris