You might ought to look at the Flash Communication Server.

It is pretty easy to construct a Perl wrapper around the ActionScripting, if you want to control and create the SWF files with Perl.

A Perl wrapper can compile the SWF files in Flash MX 2004.

If you use alot of ActionScript #include directives, Perl can rewrite the FLA files as needed.

Perl can easily write config files in XML and LoadVars that SWF file can read.

There is also the FLAP (FLAsh remoting in Perl), which I have never used but looks super useful.