You don't say where you set that. Control Panel, System, Advanced, Environment Variables perhaps? PATH components I have there propagate to Terminator. If, however, I try to use % substitution there - prepending "%HOME%\bin;" - then I see that (unsubstituted) in "the Cygwin terminal" and rxvt. If I open a new Terminator window, by eg double-clicking on the desktop shortcut, then my change has no effect, because that just tells the existing Terminator process to open a new window. If I quit all the Terminator windows and double-click again, then I see the %HOME%/bin component (unsubstituted). So I suspect you've been caught out by the optimization that turns a new application invocation into a new window request.
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