Sounds odd indeed ... are you delivering the *exact same* HTML via the CGI and via the static page?

Evidently, the version generated by your script is describing the applet in such a way as to make it think it's supposed to execute it (which is what you suspect) but if that's not happening with the static HTML the first place to look is in how the <applet> tags look.

I'd move the applet to a different directory, you may have them in a directory which Apache has marked with the Options +ExecCGI switch.

Philosophy can be made out of anything. Or less -- Jerry A. Fodor