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Ah. That would explain it, since the macro values you pass in become temporary macros (which override project macros) and there is no way, when passed on the command-line, to specify that the temporary macros update env vars.
One workaround would be to migrate your batch file code into VBP projects. Then you wouldn't have to worry about setting env vars.
Another option would be to pass in the temp macros under a slightly different name (i.e, prefixed with _ or x), then add Set Macro steps at the start of the build to set the real temp macros (marked to update env vars, these will override the project macros) from the alternate temp macros only if the alternate temp macro exists. When such a Set Macro step is executed during a build, it also updates the environment block with that macro's value.
Something we'll consider doing, which would probably solve the problem, would be to add a command-line flag to indicate that all temporary macros being passed should be marked to update env vars.
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