MSConfig does not show you all programs that are running at startup. That's my experience, anyway. There are other alternatives, and free at that. I use "Startup Control Panel", which, when installed, puts an icon in your Control Panel labeled "Startup". Once you open that, you'll see a box with multiple tabs that shows you what locations these programs are running from (registry, or Statup menu, etc.)

See the screenshot and download/install from here:

http://www.mlin.net/StartupCPL.shtml

Note the differences between the installer located in the zip file (which installs the program to Control Panel) or the "Standalone EXE" file, which you just put in any folder you want and run it from there.
I use the Control Panel version, but both do the same thing.

There is a more sophisticated app --also free-- from sysinternals that goes quite a bit deeper. It's called Autoruns. Here it is:

http://technet.microsoft.com/en-us/sysinternals/bb963902.aspx

At first glance, it looks like it's for "Windows 95", but it's actually "Autoruns for Windows" Version 9.5. You need to be careful with this app, as you could easily untoggle stuff you shouldn't.

Now, as far as your problem goes, I'm thinking there might be other or older versions of mouse software running that's preventing the Logitech stuff. So, take a look at Startup Control Panel and see exactly what's running.