The easiest fix would be to remove it from the start menu. That way it wouldn't start when you boot and therefore you wouldn't get that message on booting.
I recommend you use startup Inspector to regulate your start menu as it is much simpler to use than msconfig (which was designed by MS for troubleshooting anyway and not for permamently removing things from the start menu).
Startup Inspector
And
Startup Monitor
http://www.windowsstartup.com/download.php
While you're there, get Startup Monitor too. It is a small ap that will notify you if any ap tries to load itself into your start menu and give you the choice to let it do so or not.
If you have Spybot, there is a similar tool to remove start menu items in it.
After you remove Word Perfect from the start menu - reboot. You should not see the warning anymore.
To see if you have some corruption in Word Perfect, open it from your programs menu.
If it opens - fine. If not you may need to uninstall it and reinstall it again or repair it.