I don't use the stock mms app, I use chomp. When I open messaging it slows my phone to a crawl until I reboot, its done it as far back as I remember. Would this affect that?
I believe the Modified Apps are already installed and running - and if you run the script it will install the (un) modified apps - if you look in the Music Application and see the transparent backdrop, this is the Modified music app, install the other and that backdrop becomes solid - also the browser has an option to Invert the colors in the settings, this is also the Modified Version -