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Without seeing how the code you are using I can only speculate, but this script step example demonstrates something similar, in vb script it creates a macro (and makes it available as an environment variable) then invokes cmd.exe. If I type SET in that instance of cmd.exe, the macro is listed as an environment variable.
If this doesn't help, please provide more detai on how you are invoking this external application.
<step action='Run Script' type='0'>
<Language>VBScript</Language>
<Script><![CDATA[Set objMacroColl = Application.Macros(vbldMacroTemporary)
objMacroColl.Add "ENV_MACRO", "ENV_MACRO value", , , True
Set WshShell = CreateObject("WScript.Shell")
WshShell.Run "cmd.exe"]]></Script>
<indent type='3'>1</indent>
<name>Test script step</name>
</step>
Note: just copy/paste the above xml fragment into Visual Build Pro for a step that you can review/use.
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