Your webserver returns the wrong content-type header or your Perl scripts don't return content-type:text/html headers, most likely because you are not using the CGI.pm module.
That a DOS window (in fact, it's just a console window, but the term DOS window is more common) opens, is natural, as Windows starts Perl.exe to open/execute the file that was downloaded as .pl file, and Perl is connected to the .pl file extension. So check that your MIME types in your webserver are correct and that your scripts are also generating the right content-type headers.
And use CGI !
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Silly question: are you accessing Perl scripts through a webserver
(that is, <samp>http://localhost/myscript.pl</samp>) or are you
accessing them through Windows Explorer (<samp>C:\InetPub\wwwroot\myscript.pl</samp>)?
It sounds like the latter.
It makes a world of difference. Windows explorer runs the Perl scripts as if they were run
from a command shell. Your webserver runs them with the appropriate environment values set and
querie parameters sent, filters the output, and sends it to the web browser.
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