I keep running into issues with a server timeout error and also fatal
errors about redeclaring GetQSitem in the settings.php file.  Some
queries only have 3 records and some have 10,000 records.  I have
rebooted my server what i don't understand is that it was working
yesterday fine.  nothing has changed to the coding.  Please advise i
have an entire company using this system to run business.

I have resolved the issue by change require("settings.php") to 
require_once("settings.php")

Also the fatal errors was resolved by un-setting the $_SESSION['ex3'] 
after the query has executed