authentication breaks some .cgi scripts

I've reviewed applying both Digest and Basic authenticatin for my home page and both work fine, however, some Perl based CGI's don't work with authentication of any type, once activated. but are fine once I uncomment the offending lines in the .conf

All other static pages work fine with authentication.

Do you know why this may be?

in the httpd.conf file, I tried.

# for digest
 <Directory "C:/Apache2/htdocs">
 AuthType Digest
 AuthName "MyRealm"
 AuthDigestFile "C:/Apache2/passwd/cypher.txt"
 require user admin
</Directory>

 - and -

# for basic
 <Directory "C:/Apache2/htdocs">
 AuthType Basic
 AuthName "MySite"
 AuthDigestFile "C:/Apache2/passwd/basic.txt"
 require user admin
 </Directory>