OP wrote 'For whatever reason, the copy of, "Config.pm" in the, "_vti_cnf" dir"...' prompting me to wonder if (shifting voice to "direct address"):

• you are putting it there (intentionally or otherwise)?
    or
• you believe the presence of config.pm to be an "automatic" feature of FP?
    or
• the source for what FP pretends is .html may include some sort of reference to config.pm?

Based solely on the limited info you've provided, I suspect the problem lies in your selection of and linking (eg, coding) to <dir> names, but I'm so rabidly anti-FP that YMMV.