Please provide the manufacturer, name and version of the software you are trying to install. Is it from a download that is saved on your desktop or is it a CD or are you trying to install it directly from the internet or an internal network? If a download, please provide the link where you got it and if a download or internal network, where it is currently saved (the full path).
I'm sorry if this comes across wrong (I mean nothing personal by it), but are you absolutely certain you are logged in as an administrator when you are doing this (many people have multiple accounts and sometimes login to the wrong one by accident)? Even still, the run as administrator should have worked if even if you weren't (though it would have requested your admin password) - so that probably isn't the issue.
Go to Start / Control Panel / User Accounts and confirm that the tag under your name says Administrator. I want to make sure that somehow the system hasn't changed your account to a standard user account (I've seen it happen to others).
Try downloading Autoruns: Autoruns for Windows
(it's a good program to have and use instead of msconfig) and see if that will install and run. I'm trying to see if the problem is with the program you are trying to install or with the installation procedure itself (or your status as an administrator).
If the above doesn't identify a problem, then I'll try to check the actual software on the web site (assuming it was a download and not a CD and once you provide it) and see if I can find anything there that might explain things.
I hope this helps or at least helps lead us to identifying the cause and from there a solution.
Thanks and good luck!