Some more info to add here and I hope someone can start me in the right direction.
Rebuilt the server:
1-Ubuntu Server 9.10 using LAMP and OpenSSH options
2-Installed OA SVN trunk
3-used audit.vbs to audit domain
AT THIS POINT EVERYTHING WORKS

4-installed phpMyAdmin to backup mySQL and other SQL tasks not much of a DBA
5-ran NMAP_LINUX.sh script
6-no errors
7-modified NAMP script
8-ran with errors
Went to main page and the links and totals don't work again????

Wish I had checked the main page between steps 4 &5 and after step 6. Now I am not sure what broke things.
new script
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#!/bin/bash
for ((a=1; a <= 254 ; a++))
do
echo "$1$a"
nmap_file="nmap_file.txt"
nmap -v -O -oN $nmap_file $1$a
nmap_output='cat $nmap_file'
wget -q --post-data="submit=submit&add=$nmap_output"
http://172.20.221.21/admin$rm "$nmap_file"
rm "admin_nmap_input.php"
done
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tried to make it use a command line variable for the subnet.
any ideas?
Doug
Wish I had checked