If you only have the one site on your server then please disregard this message. The following is for FP98 extensions, so the dialog and procedure may differ slightly:
The extensions can be thought of as a two-stage process. The first stage adds the extensions to the NT environment. It only has to be performed once, does not change any sites, and is not an upgrade -- different sites on the same server can run different versions.
The second part of installing has to do with telling IIS which websites use which extensions.
Click on Start->Programs->Windows NT 4.0 Option Pack->Microsoft Internet Information Server->FrontPage Server Administrator.
You should see the familiar (if not unintuitive) FrontPage Admin screen.
The listbox at the top left shows the sites (by their descriptive name from the IIS properties page) that have *any* FrontPage server extensions installed. These are sites -- remember the two stages? This is the second stage.
If the site you are working with (be sure you understand what I am saying here) is listed, make sure it is highlighted when you press Upgrade. If this is what you did before, Uninstall it.
If the site isn't listed here (or if you just did the Uninstall from the last step), press Install and find your way to the listing of sites in IIS by answering the Server Type dialog appropriately. Select your site and press OK. At this point, the extensions are installed and enabled for the site.
As you change the selectionin the text box, the Server, Content and Version information will change appropriately to reflect the selected site. (Ensure Authoring is enabled on the site you are working with).
Run a check & fix but don't let FP change the security settings.