I've noticed that when you add a script map in IIS 7, IIS will alter your web.config and actually remove values it has nothing to do with.
For example,
<applicationSettings>
<Dealers.Web.Properties.Settings>
<setting name="Dealers_Web_UserAgentsService_UserAgentsService"
serializeAs="String">
<value>http://useragents.vertagen.com/UserAgentsService.asmx</value>
</setting>
</Dealers.Web.Properties.Settings>
</applicationSettings>
Is changed to
<applicationSettings>
<Dealers.Web.Properties.Settings>
<setting name="Dealers_Web_UserAgentsService_UserAgentsService" serializeAs="String">
<value></value>
</setting>
</Dealers.Web.Properties.Settings>
</applicationSettings>
It appears that if IIS sees any value in your web.config that is stored in a <tag>value</tag> format, it will strip the value out.
I think its easy to see that this is a serious problem, does anyone know if there's a work-around or patch available?