Hi, I had the same issue but I fix that. The problem is in "Packages/Default/exec.py" file that is responsible for builds. It's loading just User/Defaul settings but not a syntax specific settings.
To fix that I change this (line 133):
show_panel_on_build = sublime.load_settings("Preferences.sublime-settings").get("show_panel_on_build", True)
show_panel_on_build = self.window.active_view().settings().get('show_panel_on_build', True)
and it's work now.
However I notice that few lines below it's actually load syntax specifics settings but just for "build_env" entry. It's also checks whether "self.window.active_view()" exists before getting that entry. That's probably mean that active_view is not available in some cases.
Could someone please explain how it is? and why it's not loading syntax specific settings on default?