My guess is that you 'deleted' the site  from the 'Manage Sites' page which
is only a list and did not go to the site itself and delete the site from
within the Top-Level Site Administration page(
http://[yourportalservername]/sites/[yoursitename]/_layouts/1033/webadmin.aspx )
. You should get in the habit of deleting the site before deleting the
llisting. I posted tip on MSD2D that can help in the situation:
www.msd2d.com/.../Tip_viewitem_03.aspx

To solve your current problem you will have to use stsadm.exe to remove the
site by running:

C:\Program Files\Common Files\Microsoft Shared\web server
extensions\60\BIN>stsadm.exe -o deletesite -url
http://[yourportalservername]/sites/[yoursitename]

Maybe some command line goodness is all you need:

list your top level sites: see if you can locate it there
stsadm -o enumsites -url http://yourportal

you should see it then delete with this:
stsadm -o deletesite -url http://yourportal/sites/yourhiddensite

stsadm is in "c:\\Program Files\Common Files\Microsoft Shared\web server
extensions\60\BIN"

OR

Slight chance that you need to check managed path to make sure you
didn't make an exclusion:
From the "SharePoint portal  Server Central Administration", click
"Configure virtual server  settings from the Virtual Server List page"
click your virtual server, then "Define managed paths" - check to see if
the URL you are using is being excluded.

I tried running the stsadm command and it comes back with "The server  instance specified was not found. Please specify the server's address and port." I have added the correct url after the -url switch. Any suggestions? Thanks

try using the servername.......