The crontab entry ...

* * * * * /home/httpd/vhosts/mysite.com/cgi-bin/deleteFiles.pl?documen
+troot=/home/user/directory
[download]

... could of been writen like so ...

* * * * * wget http://mysite.com/cgi-bin/deleteFiles.pl?documentroot=/
+home/user/directory
[download]

The crontab entry ...

* * * * * /home/httpd/vhosts/mysite.com/cgi-bin/deleteFiles.pl /home/u
+ser/directory
[download]

... could of been writen like so ...

* * * * * /home/httpd/vhosts/mysite.com/cgi-bin/deleteFiles.pl documen
+troot=/home/user/directory
[download]

Your print debug statement should look like this ...

print "doc=[$documentroot]\n";
[download]