Duplicate config sections in web.config and internal server errors...

There is a duplicate 'myApp' section defined, Internal Server Error

Had a breakdown moment today when two sites didn't behave. Each site had a virtual application with its own web.config.
Both sites where configured almost the same but one of the virtual applications worked and not the other.
The following error was displayed.

HTTP Error 500.19 - Internal Server Error

The requested page cannot be accessed because the related configuration data for the page is invalid.

Detailed Error Information:

Module           IIS Web Core
Notification     BeginRequest
Handler          Not yet determined
Error Code       0x800700b7
Config Error     There is a duplicate 'myapp' section defined
Config File      \\?\c:\MyApp\vapp\web.config
Requested URL    http://myapp:80/vapp/
Physical Path    c:\MyApp\
Logon Method     Not yet determined
Logon User       Not yet determined

Config Source:
    7:   <configsections>
    8:     <section name="myApp" type="MyApp.MyConfigSection, MyApp"/>
    9:   </configsections>

This configuration section was present in my site as well, like below.

<section name="myApp" type="MyApp.MyConfigSection,MyApp"/>

Removing the section from the vapp did the trick, but why did it work on the other site?

Finally after some testing and borrowing a second pair of eyes (thx robert), a small difference in the setup was detected. One of the sections where declared with the type "MyApp.MyConfigSection, MyApp" and the other with "MyApp.MyConfigSection,MyApp". Did you see it?! A small whitespace between the type and assembly names where missing.
After adjusting the typo to either keeping the whitespace or removing it on both, it started to work...