In my script the BASEURL configurable lineat the top is very important.
Lets say you originally installed a SC client and while doing this you visited your site at
http://www.mysite.com/host to create the installer. This will create the service and installer pointing to
www.mysite.com. Now lets say you use my script to do and upgrade and in the BASEURL line you use
http://mysite.com. This will create a second instance of SC on the machine and point it to mysite.com.
I had an internal machine like this myself because of exactly what I described here. The easiest way to cleanup the service is to just run regedit and navigate to HKLM/SYSTEM/CurrentControlSet/Services and delete the offending entry. You will need to reboot for the entry to not be shown in windows anymore.
Not sure what is going on with your second issue.
Hope this explains things.