I've been battling with this as well. I found that my problem was that the IIS user did not have read and execute permissions on the directory containing the programs I was trying to backtick execute. Here's my test program:

#!c:\Tools\perl\5.6.1\bin\MSWin32-x86\perl.exe
use CGI qw/:standard/;
$ENV{PATH} = "C:\\httpdocs;"; 
$| = 1;
print header;
print `dir`;
[download]

Inside of C:\httpdocs, I put a copy of cmd.exe. On the C:\httpdocs directory, I gave the IIS user "read & execute," "list folder contents" and "read" permissions. After that, the test started working. Good luck, Mike P.S. If your scripts write to a file, be sure the IIS user has write permissions on the target directory.