MMOViper doesnt change files, it injects a hook. It could be that in your system the hook never gets removed from the game which would require a reboot to uninject it. It is a global inject so that even if you close the game and reopenit, the injected file might still be running in your system.
Nobody else is having similar issues, so it could just be something specific to your system. Well, the only time a person has reported lag was when he had a patrol that was HUGE. If you have a really big patrol area, try a smaller one and see if that helps.
Summary, reboot after running viper, and your system will be as if viper was never installed.
PS, Viper has never been reported as a trojan. If you are getting a message like that, you indeed may have a virus/trojan in your system that is trying to infect your copy of viper.