After I moved the MojoPortal files to the root, and edited the Mojoportal WEB.CONFIG file adding the section:

<location path="." inheritInChildApplications="false">
</location>

around the <system.web>...</system.web> section. 

Would anyone know why I now get the following error in my sub application?

Server Error in '/MyCustomApp' Application.

Could not load file or assembly 'mojoPortal.Web' or one of its dependencies. The system cannot find the file specified.

Description: An unhandled exception occurred during the execution of the current web request. Please review the stack trace for more information about the error and where it originated in the code.

Exception Details: System.IO.FileNotFoundException: Could not load file or assembly 'mojoPortal.Web' or one of its dependencies. The system cannot find the file specified.

Source Error:

An unhandled exception was generated during the execution of the current web request. Information regarding the origin and location of the exception can be identified using the exception stack trace below.

Assembly Load Trace: The following information can be helpful to determine why the assembly 'mojoPortal.Web' could not be loaded.

WRN: Assembly binding logging is turned OFF.To enable assembly bind failure logging, set the registry value [HKLM\Software\Microsoft\Fusion!EnableLog] (DWORD) to 1.Note: There is some performance penalty associated with assembly bind failure logging.To turn this feature off, remove the registry value [HKLM\Software\Microsoft\Fusion!EnableLog].

Stack Trace:

[FileNotFoundException: Could not load file or assembly 'mojoPortal.Web' or one of its dependencies. The system cannot find the file specified.] System.RuntimeTypeHandle._GetTypeByName(String name, Boolean throwOnError, Boolean ignoreCase, Boolean reflectionOnly, StackCrawlMark& stackMark, Boolean loadTypeFromPartialName) +0 System.RuntimeTypeHandle.GetTypeByName(String name, Boolean throwOnError, Boolean ignoreCase, Boolean reflectionOnly, StackCrawlMark& stackMark) +64 System.RuntimeType.PrivateGetType(String typeName, Boolean throwOnError, Boolean ignoreCase, Boolean reflectionOnly, StackCrawlMark& stackMark) +58 System.Type.GetType(String typeName, Boolean throwOnError, Boolean ignoreCase) +65 System.Web.Compilation.BuildManager.GetType(String typeName, Boolean throwOnError, Boolean ignoreCase) +342 System.Web.Configuration.ConfigUtil.GetType(String typeName, String propertyName, ConfigurationElement configElement, XmlNode node, Boolean checkAptcaBit, Boolean ignoreCase) +52

So in removed the application configuration from IIS - and received a more generic web.config error "An error occurred reading the integrated module list from system.webServer/modules. The error is 0x80070021."

Then I setup the app again "This folder is setup as a web application" and received the same error "Server Error in '/MyCustomApp' Application. Could not load file or assembly 'mojoPortal.Web' or one of its dependencies. The system cannot find the file specified."

Restarted the IIS server and also recycled the app pool.  No luck.

Removed the path="*" from the <location> tag, no luck.

Unwrapped the <location> tag from <system.web> (<location inheritInChildApplications="false"></location>) no luck.

In all cases Mojoportal is working either at the root or in the /mojoportal subfolder I created - and myCustomApp is only working when Mojoportal is in the subfolder.

Any other ideas?

Both apps are .NET 3.5

I've tried Integrated Application Pool and Classic - no luck

Any other ideas? 

I just upgraded to the latest version of mojoportal and instantly my custom app failed.

After searching through this forum I kept landing on this thread over and over until I found another thread that indicated what I had to do.  I've added a reply here because this is where google kept sending me. Probably because I'm also with DiscountASP.Net (which is normally rocking for MojoPortal hosting).

In addition to the <location path="."  inheritInChildApplications="false"> around <system.web>  tag

I also needed this:

<location inheritInChildApplications="false"> around  <system.webServer>

At that point everything just worked.  Otherwise I kept getting:

"Could not load file or assembly 'mojoPortal.Web' or one of its dependencies." as per Joe Vago's post.

No - that article and the links don't mention system.webserver.  Both only mention system.web, which is all that was required with the previous version of mojoportal I had installed (or maybe more accurately, it is all that was required with the previous web.config).

Here's the only reference where I can see you wrote that the location wrapper "should also wrap system.webserver section"

http://www.mojoportal.com/Forums/Thread.aspx?pageid=5&mid=34&ItemID=9&thread=6206&pagenumber=1

I couldn't find that requirement for system.webserver listed anywhere else.

Can I suggest that you add in the location tags in the distributed web.confg?  That ensures that ASP.Net applications will work under mojoportal without affecting the running of mojoportal and without the developer having to touch the web.config to make it happen.

Thanks again for a great product,

Philip