私がしたことは、BlogEngen.Netのweb.configファイルの最後にロケーションタグを追加して、サブフォルダーの設定を削除したことです。
<location path="wiki" allowOverride="true">
<connectionStrings>
<remove name="BlogEngine"/>
<add name="LocalSqlServer" connectionString="data source=.\SQLEXPRESS;Integrated Security=SSPI;AttachDBFilename=|DataDirectory|aspnetdb.mdf;User Instance=true" providerName="System.Data.SqlClient"/>
</connectionStrings>
<system.web>
<compilation debug="false" targetFramework="4.0">
<assemblies>
<remove assembly="System.Management, Version=4.0.0.0, Culture=neutral, PublicKeyToken=B03F5F7F11D50A3A"/>
<remove assembly="System.Configuration, Version=4.0.0.0, Culture=neutral, PublicKeyToken=B03F5F7F11D50A3A"/>
<remove assembly="System.Data, Version=4.0.0.0, Culture=neutral, PublicKeyToken=B77A5C561934E089"/>
<remove assembly="System, Version=4.0.0.0, Culture=neutral, PublicKeyToken=B77A5C561934E089"/>
<remove assembly="System.Drawing, Version=4.0.0.0, Culture=neutral, PublicKeyToken=B03F5F7F11D50A3A"/>
<remove assembly="System.Web, Version=4.0.0.0, Culture=neutral, PublicKeyToken=B03F5F7F11D50A3A"/>
<remove assembly="System.Xml, Version=4.0.0.0, Culture=neutral, PublicKeyToken=B77A5C561934E089"/>
<remove assembly="Microsoft.Web.Infrastructure, Version=1.0.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35"/>
<remove assembly="System.Web.Razor, Version=1.0.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35"/>
<remove assembly="System.Web.WebPages, Version=1.0.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35"/>
<remove assembly="System.Web.WebPages.Razor, Version=1.0.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35"/>
<remove assembly="System.Web.Helpers, Version=1.0.0.0, Culture=neutral, PublicKeyToken=31BF3856AD364E35"/>
</assemblies>
<expressionBuilders>
<remove expressionPrefix="LinqLength"/>
<remove expressionPrefix="Reflect"/>
<remove expressionPrefix="Session"/>
<remove expressionPrefix="Server"/>
<remove expressionPrefix="QueryString"/>
<remove expressionPrefix="Code"/>
</expressionBuilders>
</compilation>
<membership defaultProvider="AspNetSqlMembershipProvider">
<providers>
<clear/>
<add name="AspNetSqlMembershipProvider" type="System.Web.Security.SqlMembershipProvider, System.Web, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a" connectionStringName="LocalSqlServer" enablePasswordRetrieval="false" enablePasswordReset="true" requiresQuestionAndAnswer="true" applicationName="/" requiresUniqueEmail="false" passwordFormat="Hashed" maxInvalidPasswordAttempts="5" minRequiredPasswordLength="7" minRequiredNonalphanumericCharacters="1" passwordAttemptWindow="10" passwordStrengthRegularExpression=""/>
</providers>
</membership>
<roleManager defaultProvider="AspNetSqlRoleProvider">
<providers>
<clear/>
<add name="AspNetSqlRoleProvider" connectionStringName="LocalSqlServer" applicationName="/" type="System.Web.Security.SqlRoleProvider, System.Web, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a"/>
<add name="AspNetWindowsTokenRoleProvider" applicationName="/" type="System.Web.Security.WindowsTokenRoleProvider, System.Web, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a"/>
</providers>
</roleManager>
<siteMap defaultProvider="AspNetXmlSiteMapProvider">
<providers>
<add siteMapFile="web.sitemap" name="AspNetXmlSiteMapProvider" type="System.Web.XmlSiteMapProvider, System.Web, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a" />
</providers>
</siteMap>
<httpModules>
<remove name="WwwSubDomainModule"/>
<remove name="UrlRewrite"/>
<remove name="CompressionModule"/>
<remove name="ReferrerModule"/>
<remove name="SecurityModule"/>
<remove name="RightModule"/>
</httpModules>
<httpHandlers>
<remove verb="*" path="file.axd"/>
<remove verb="*" path="image.axd"/>
<remove verb="*" path="syndication.axd"/>
<remove verb="*" path="sitemap.axd"/>
<remove verb="*" path="trackback.axd"/>
<remove verb="*" path="pingback.axd"/>
<remove verb="*" path="opensearch.axd"/>
<remove verb="*" path="metaweblog.axd"/>
<remove verb="*" path="rsd.axd"/>
<remove verb="*" path="css.axd"/>
<remove verb="*" path="js.axd"/>
<remove verb="*" path="res.axd"/>
<remove verb="*" path="rating.axd"/>
<remove verb="*" path="opml.axd"/>
<remove verb="*" path="blogml.axd"/>
<remove verb="*" path="sioc.axd"/>
<remove verb="*" path="apml.axd"/>
<remove verb="*" path="foaf*.axd"/>
<remove verb="*" path="*.htm"/>
</httpHandlers>
</system.web>
<system.webServer>
<modules>
<remove name="WwwSubDomainModule"/>
<remove name="UrlRewrite"/>
<remove name="CompressionModule"/>
<remove name="ReferrerModule"/>
<remove name="SecurityModule"/>
<remove name="RightModule"/>
</modules>
<handlers>
<remove name="FileHandler"/>
<remove name="ImageHandler"/>
<remove name="Syndication"/>
<remove name="Sitemap"/>
<remove name="Trackback"/>
<remove name="Pingback"/>
<remove name="OpenSearch"/>
<remove name="MetaWeblog"/>
<remove name="RSD"/>
<remove name="CssHandler"/>
<remove name="Javascript"/>
<remove name="Resource"/>
<remove name="Rating"/>
<remove name="Opml"/>
<remove name="BlogML"/>
<remove name="SIOC"/>
<remove name="Apml"/>
<remove name="Foaf"/>
<remove name="Html"/>
</handlers>
</system.webServer>
これを使用し、さらにサブフォルダーがある場合は、それぞれに追加する必要があります。