Configuration System Failed to Initialize

This is a bit late I know but when I remove this:

<startup>
   <supportedRuntime version="v4.0" sku=".NETFramework,Version=v4.6" />
</startup>

then the error disappears.

Try putting the configSections as the first child element of configuration, because configSections should be the first element of configurations

So your config file will go like this:

<configuration>

  <configSections>
    <sectionGroup name="userSettings" type="System.Configuration.UserSettingsGroup, System, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089">
      <section name="Vegi_Manager.Properties.Settings" type="System.Configuration.ClientSettingsSection, System, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" allowExeDefinition="MachineToLocalUser" requirePermission="false"/>
    </sectionGroup>
  </configSections>

  <connectionStrings>
    <add name="ConStr" connectionString="Integrated Security=false;Persist Security Info=False;User ID=funny;password=veryfunny;Initial Catalog=vegimanager;Data Source=.\sqlexpress;"/>
  </connectionStrings>

  <userSettings>
    <Vegi_Manager.Properties.Settings>
      <setting name="FIRMNAME" serializeAs="String">
        <value/>
      </setting>
      <setting name="FIRMADDRESS" serializeAs="String">
        <value/>
      </setting>
      <setting name="FIRMCITY" serializeAs="String">
        <value/>
      </setting>
      <setting name="FIRMSTATE" serializeAs="String">
        <value/>
      </setting>
      <setting name="FIRMPHONE" serializeAs="String">
        <value/>
      </setting>
      <setting name="FIRMMOBILE" serializeAs="String">
        <value/>
      </setting>
      <setting name="FIRMEMAIL" serializeAs="String">
        <value/>
      </setting>
      <setting name="FIRMTIN" serializeAs="String">
        <value/>
      </setting>
      <setting name="FIRMPAN" serializeAs="String">
        <value/>
      </setting>
      <setting name="FIRMMANDITAXNO" serializeAs="String">
        <value/>
      </setting>
      <setting name="INITIALFONFIGDONE" serializeAs="String">
        <value>False</value>
      </setting>
      <setting name="FIRMJURISDICTION" serializeAs="String">
        <value/>
      </setting>
      <setting name="FIRMBANKDETAILS" serializeAs="String">
        <value/>
      </setting>
      <setting name="FIRMDETAILS" serializeAs="String">
        <value/>
      </setting>
      <setting name="BILLFORMATNO" serializeAs="String">
        <value>0</value>
      </setting>
      <setting name="PRINTERNAME" serializeAs="String">
        <value/>
      </setting>
    </Vegi_Manager.Properties.Settings>
  </userSettings>

  <startup>
    <supportedRuntime version="v4.0" sku=".NETFramework,Version=v4.0"/>
  </startup>
</configuration>