Problem with Virtual Hosts Individual Config Files and OSX 10.7 Lion (AllowOverride Setting)

I am hoping some other Xserve users running OSX 10.7 (Lion) can offer some additional input or help in a couple of issues I am running into with the Apache settings on my server.
Below is an example site config file on our server. We are hosting a number of sites and are using .htaccess files and apache's rewrite module to create vanity URLs. In order for the .htaccess files to be used AllowOverride has to be set to "All" instead of "None"
The problem I am running into is everytime I stop and restart the web service on the machine it keeps changing this setting back in the individual site configuration files. I will change it to AllowOverride All and next time the server has to be restarted or the web service has to be restarted it is defaulting every site back to None which has become quite frustrating.
Is there somewhere I can set this default setting to prevent this from occuring and forcing every site and site config to default to "AllowOverride All" ?
Should I be researching this somewhere specific? OSX 10.7 changed the entire Apache Interface and the manner in which it runs and I am finding little to no documentation on it.

Are you using the default Server.app, or have you downloaded and installed the (proper) Server Admin tools?
Server Admin.app isn't included as part of the Lion Server distribution, but if you download it and install it you get the same set of admin tools as you're used to with previous versions. From there you should be able to set the 'Allow All Overrides' setting for your site.

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