Google apparently knows and loves the .html page. However, it knows nothing about the .pl page. So until it comes and sees what the pages is all about, targeting will likely be off (or non-existent).

If you switch all your pages from .html to .pl, it's likely that you will take a short-term hit until Google comes back and re-checks all the pages.

An alternative that you may want to look into instead is telling your application server to process all your .html pages as if they had a .pl extension. (In other words, the default setup is that your web server processes .html pages directly, while all .pl pages first get processed through the PERL application server then get passed to the web server. You would configure your PERL application server to processes all .html and .pl files before sending to the web server.) How you actually do that depends on what web server/OS you're using.

I know its sounds kinda sketchy but have you tried an external Adwords account and targeting your site manually to see if you get impressions?

It can make a difference to volume but have you set that the channel can be targeted by advertisers?

Check the page headers. Ads are also not served for pages with mobile headers (text/vnd.wap.wml, etc.)

try

#!/usr/bin/perl
  print "Content-type: text/html\r\n\r\n";

IMHO if you have doubt that adsense is showing relevant ads only on html pages (highly unlikely IMO) then try using .htaccess file to redirect html page request to your .pl pages.
I am no pearl expert but is this possible?

Thanks
Rajiv