> it seems that Ctx [re]defines the system variable HOME on its run;

This is not an answer, but a guess: Could it be that your interactive
shell uses one setting, and the non-interactive shell uses another?
I'm only guessing here, I don't know much about Windows
administration; I just remember being driven to despair by a similar
'these settings are not used if the shell is not interactive' problem
under Linux.

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