I know i'm responding to a quite old question, but this is just in case it can help anyone. After trying to upgrade 6.9.4 to 6.9.8 without success using the MySql installer, i found out that the process is quite dependant on the machine.config contents. In my case, my machine config had this element commented:
<system.web>
<membership>
<providers>
<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="" />
<!--add name="MySQLMembershipProvider" type="MySql.Web.Security.MySQLMembershipProvider, MySql.Web.v20, Version=6.9.4.0, Culture=neutral, PublicKeyToken=c5687fc88969c44d" connectionStringName="LocalMySqlServer" enablePasswordRetrieval="false" enablePasswordReset="true" requiresQuestionAndAnswer="true" applicationName="/" requiresUniqueEmail="false" passwordFormat="Clear" maxInvalidPasswordAttempts="5" minRequiredPasswordLength="7" minRequiredNonalphanumericCharacters="1" passwordAttemptWindow="10" passwordStrengthRegularExpression="" /-->
</providers>
I just deleted the commented element and the mysql installer process ran withouth errors.
To find machine config in your system:Where Is Machine.Config?