Running a program via CGI is very different from running a program from command line, and also has much more security issues.

summary:

#!/usr/bin/perl -wT
use CGI;
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Update:

After reading your post again, it seems your problem is indeed related to permissions. Make shure the files are writeable for the user the webserver is running as.

Try checking the results of your system call like this:

system("command ...") == 0 or die "System error: $?";
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You could also take a look at the error logs and see the error code your script outputs.

-- 
Joost       downtime n. The period during which a system
            is error-free and immune from user input.
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