I solved this by putting:

<script runat="server">
void Application_Start(object sender, EventArgs e)
{
var provider = new ElencySolutions.ImageMap.Properties.RegisterResources.Start();
}

</script>

in global.asax. 

Resources:

http://stackoverflow.com/questions/3601228/custom-virtualpathprovider-not-being-used-in-iis6

http://forums.asp.net/t/995633.aspx

http://stackoverflow.com/questions/4266314/how-can-i-fix-a-2104-error-in-a-silverlight-application

The post above worked for a while, but I managed to change global.asax by mistake and then it didn't work no more.

I changed to what was working previously, but I keep getting error about protection level on RegisterResources which is an internal function.

The method Start inside RegisterResources is however public, but the class overrides this.

I copied all the code regarding registering the resources into global.asax. After that, I did't get an error when I'm opening the editorial window for ImageMap:

System.ArgumentNullException: Value cannot be null.
Parameter name: stream

Stack trace:

[ArgumentNullException: Value cannot be null.
Parameter name: stream]
System.IO.StreamReader..ctor(Stream stream, Encoding encoding, Boolean detectEncodingFromByteOrderMarks, Int32 bufferSize) +9431625
System.Web.UI.TemplateParser.ParseFile(String physicalPath, VirtualPath virtualPath) +232
System.Web.UI.TemplateParser.ParseInternal() +86
System.Web.UI.TemplateParser.Parse() +160
System.Web.Compilation.BaseTemplateBuildProvider.get_CodeCompilerType() +110
System.Web.Compilation.BuildProvider.GetCompilerTypeFromBuildProvider(BuildProvider buildProvider) +65
System.Web.Compilation.BuildProvidersCompiler.ProcessBuildProviders() +218
System.Web.Compilation.BuildProvidersCompiler.PerformBuild() +40
System.Web.Compilation.BuildManager.CompileWebFile(VirtualPath virtualPath) +9098998
System.Web.Compilation.BuildManager.GetVPathBuildResultInternal(VirtualPath virtualPath, Boolean noBuild, Boolean allowCrossApp, Boolean allowBuildInPrecompile, Boolean throwIfNotFound, Boolean ensureIsUpToDate) +320
System.Web.Compilation.BuildManager.GetVPathBuildResultWithNoAssert(HttpContext context, VirtualPath virtualPath, Boolean noBuild, Boolean allowCrossApp, Boolean allowBuildInPrecompile, Boolean throwIfNotFound, Boolean ensureIsUpToDate) +111
System.Web.Compilation.BuildManager.GetVirtualPathObjectFactory(VirtualPath virtualPath, HttpContext context, Boolean allowCrossApp, Boolean throwIfNotFound) +125
System.Web.Compilation.BuildManager.CreateInstanceFromVirtualPath(VirtualPath virtualPath, Type requiredBaseType, HttpContext context, Boolean allowCrossApp) +52
System.Web.UI.PageHandlerFactory.GetHandlerHelper(HttpContext context, String requestType, VirtualPath virtualPath, String physicalPath) +31
System.Web.UI.PageHandlerFactory.System.Web.IHttpHandlerFactory2.GetHandler(HttpContext context, String requestType, VirtualPath virtualPath, String physicalPath) +40
System.Web.HttpApplication.MapHttpHandler(HttpContext context, String requestType, VirtualPath path, String pathTranslated, Boolean useAppConfig) +167
System.Web.MapHandlerExecutionStep.System.Web.HttpApplication.IExecutionStep.Execute() +128
System.Web.HttpApplication.ExecuteStep(IExecutionStep step, Boolean& completedSynchronously) +184

Due to an error later that caused the hole website to be down a hole day, the problem was caused by some firewall roleset.

It was therefore impossible to solve the error because I always got the same error no matter what I did.