I just created a sample virdir under my Default Web Site and I see the below entry in Metabase.xml file. Sometime, the IIS UI does not reflects the changes made in the Metabase and hence can be misleading. Check the entry
<IIsWebDirectory Location ="/LM/W3SVC/1/ROOT/samplevirdir"
I didn't had to restart IIS for the same.
Alternately, you can try Metabase Auditing to verify if the changes are really happening by following the article KB936696
Here's what I saw when I created the virdir. You see a Success Audit since I was able to create the virdir successfully.
Event Type: Success Audit
Event Source: IIS-METABASE
Event Category: Object Access
Event ID: 4505
Time: 1:05:17 AM
Metabase Set Data.
Primary User Name: Administrator
Primary User Domain: WIN-IIS2K3R2
Primary Logon ID: (0x0,0x4E05E4)
Property ID: 2102
Property Name: AppFriendlyName
Old Value: Default Application
Caller PID: 3996
Caller Image Path: \Device\HarddiskVolume1\WINDOWS\system32\mmc.exe
For more information, see Help and Support Center at http://go.microsoft.com/fwlink/events.asp.