I wouldn't use HTML::Clean on pre-parsed pages. That's your solution. I don't believe it was written to take php/asp style tags into account, only to parse either straight HTML or parsed HTML right before being output from a script.

How are you configuring HTML::Clean in your script (code please)? You can set varying "levels" and whether or not it should strip comments, which may or may not help you.

Update: Not that I particularly care (obviously I care enough to post this), but why would this node lose experience (2 votes against it, at -1 when I wrote this)? I use HTML::Clean pretty extensively, and it's not made for the weirdo tags that ASP and PHP use. What isn't helpful about this?

-Any sufficiently advanced technology is
indistinguishable from doubletalk.