Shutdown and Sleep issues

Hey guys I have been recently having issues with sleep and shut down on 10.5.7. I recently reinstalled and installed all my apps and that was when I started experiencing these problems. However, after running Onyx automated scripts things seem to be much better. I just wanted to know what could have caused these problems. Could it have been from the all the apps I installed, disk permission issues, etc. And one more thing is it normal to have a brief few seconds of slowness when you wake a mac up?

Thanks