environmentVariables ignored by FastCGI application

I need to use an environment variable to configure MapServer (http://mapserver.org/) a C program that can run as a FastCGI application in IIS.

The code uses the C getenv function to get this variable.

const char *pszCurlCABundle = NULL;
pszCurlCABundle = getenv("CURL_CA_BUNDLE");

I have set the System Environment variable in Windows and rebooted. However the variable is always null. If I run the same program from the command line the environment variable is picked up correctly.

As I understand it the FastCGI environment differs from the standard one. I have tried to configure this using IIS and applicationHost.config, but again no effect. I've tried the following at applicationHost.config and web.config levels:

<fastCgi><application fullPath="C:\Mapserver\bin\mapserv.exe"><environmentVariables><environmentVariable name="CURL_CA_BUNDLE" value="C:\Mapserver\bin\curl\curl-ca-bundle.crt" /></environmentVariables></application></fastCgi>

It seems all environment variables are null including CURL_CA_BUNDLE and path:

  test1 = getenv("Path");
  msDebug("Path=%s\n", test1); // Path=(null) 

Is this an issue with IIS, and is there anyway to set up the environment so these variables are picked up? I have tried on Windows7 and Windows Server 2008 R2, IIS 7 and IIS 7.5.7600 respectively