The FMSLogo uninstaller doesn't remove the saved FMSLogo preferences, which means that registry key is leaked if you install and then uninstall FMSLogo. For good citizenship, all traces of the installation should be removed by the uninstaller, even ones that are not normally visible.
If you install while an older version is installed (that is, if you upgrade FMSLogo), it should remove the old version, but keep/migrate your settings. If you uninstall FMSlogo, then it should remove your settings.
Leaking the preferences causes at least one user-facing problem, as the installer and uninstaller behave differently depending on the values in the registry key. The most significant of these is that if you install then uninstall FMSLogo as a standard user, then later install it as an administrator, then attempt to uninstall it as a standard user, you won't get any UI feedback that the uninstallation failed.
I think the reason for this behavior is an historical accident, not intentional. When I wrote the installation script, I wanted to share the uninstall logic between the installer and the uninstaller, in which case I wouldn't have wanted an update install to remove the preferences. This turned out to be impossible with NSIS, so the logic was duplicated anyway.
The fix will be available in the installer for version 7.0.0.