App pool user not capturing environment variables

I am running a web service under an application pool configured to run under a specific user account.

The service basically runs a script as the user the app pool is configured for.

 

There is an environment variable on the machine for that same user account to set its Clearcase_Primary_Group to %Domain%\%group%

This is because teh application required the users Clearcase Priary Group be set to a specifc dome group.

 If I log in a run the comman locally under the account in question it works fine...capture the configured environment variable..however if I run it under the service...the script runs and is definately running as the specific user..but for some reason its not picking up the environemnt variable setting the primary group.

Any idea why running as the app pool it wouldnt pick up that envrionement varibale?
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