Figured out the problem, but causing other issues.
This problem was caused by turning off inheritance in the web.config like
<location path="." inheritInChildApplications="false">
<system.web>
.......
</system.web>
</location>
Is there anyway I can get Sitebuilder to work with these settings?
Seems once I add the location to the web.config sitebuilder is unable to parse web.config correctly and unable to add to or update the current system.web
Thanks