This thread is a bit stale but in case you wanted to know...
I make no claims that this won't break something else when you edit it, but I think what you are looking for is the gPCUserExtensionNames attribute of the policy under CN={GUID of the policy},CN=Policies,CN=SYSTEM,DC=DOMAIN,DC=COM. You can edit this with ADSIEDIT.msc, etc.
It looks as if GroupPolicyEntenstions like Folder Redirection, which don't store their settings directly in registry.pol, appear to add to a list GUIDs in this attribute which is how the GPMC knows to look for the settings elsewhere. Modifying that attribute to remove the GUID for the specific part of Folder Redirection you were using, or completely removing the attribute will clear the phantom settings in GPMC. Removing the entire thing would of course remove any other gPEs too, so be careful.
It's trivial but I too found this annoying when looking at a policies and attempting to see what settings are actually set, as opposed to previously set. Nearly as annoying the as bug which MS is not patching in 2008R2 where a comment once set, cannot be blanked in the GUI (you can reduce the comment to a singe space of course). They can be removed by editing the comment.cmtx however. That has the same effect of possibly showing un-configured settings.