Wsconfig drops CFIDE virtual directory

We are running into an issue when adding sites using the wsconfig tool.  Here's our setup: Windows 2k8 R2, IIS 7.5, CF 9 multiserver configuration with 4 instances running.
We have a site all setup in IIS with a virtual directory created for CFIDE (points to c:\inetpub\wwwroot\cfide, the default/install path for cfide).  We then go into the wsconfig tool (Run As Administrator) and add this new site to an instance.  Immediately the CFIDE virtual directory disappears within IIS, whether we choose to restart IIS or not.  We check the "configure server for ColdFusion box" when adding.
I've checked the wsconfig.log, but it shows nothing, no errors, just one line "[date] [time] info Macromedia JRun 4.0 (Build 108858)" - that's it.  Everything else is fine, adds all the correct handler mappings, etc. and the site works fine, just missing cfide virtual directory which is needed as we use a couple CF tags that load JS files under there to work...
We go in afterwards and re-add the CFIDE virtual directory and it seems to stick unless we mess with wsconfig again, so we have a work-around, just an extra step and puzzled as to why this would happen.  We have hundreds of sites to setup, so would save some time to fix this.
Anyone else ever run across this situation before?

Cfarleyaz, you say you’re on “CF 9”, but can you be more specific? Technically, only CF 9.0.1 and above (9.0.2 or 10) supports IIS 7. If you’re on CF9.0, then Adobe does not formally support you running CF with IIS 7, except in IIS 6 compatibility mode. People got it to work, but it involved manual steps (perhaps including dealing what you’re noticing). 
If you are experiencing what you are with CF 9.0.1 or above, then let us know if you are running IIS in IIS 6 compat mode? It may make a difference in what someone may propose to help.
While we’re on the subject, folks should note that  things are indeed quite different about CF web server config with IIS 7 and CF 9.01 and above. For instance, it no longer works that newly created sites inherit the settings from the “all web sites” configuration. Instead (as discussed in the CF 9.0.1 doc, Configuring and Administering CF9), you have to rerun the web server config tool each time you add a new site (that you want to connect to CF).
Hope that’s helpful.
/charlie

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