Pardon me if I state the obvious, but you tried "Add/Remove," right?
If no luck there, delete the Limewire Program folder. Delete the .limewire user data folder. Download "RegSeeker" (freeware) and delete all registry entries (do a search for "Limewire").

Restart the computer. Download new version (and optionally burn to disk) - install either from the desktop downloaded version, or delete it and install from the CD copy. You should be fine.

I have been a paid "Pro" member for quite some time, and recently sent in more $$ to renew my "status." 4.10 is just terrific! But I have NEVER "upgraded" to a new version - I always uninstall completely, reinstall and then re-set prefs - and have never had LW start up unintentionally. It's a bit of a hassle I know, but if you defrag after uninstall and once again after installing new version - all the files are contiguous on the hard drive and you know you've got a "clean" start with no conflicting prefs or files from previous installs.