Hi Gee,
Welcome to the site,
I never use that auto start fuction so I am not a great one to help, but the patch shouldnt effect that.. if it worked before..
You might try going to Start > Run > type msconfig .. then click OK
Now look at the Start up tab, on that list should be the WinMx.exe file if its not on the list try reseting it in the WinMx program agian. If it is on that list make sure its ticked. Changes on Msconfig will ask you to reboot ..