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Did you try setting "Update module template .html files from themes/your theme/templates directory?" to Yes?
This is under sys admin> preferences > general settings.
Also, you may use the Themes block to see if the temes will change that way. You can enable the theme block under the sys admin>blocks menu. Then make sure you have all the themes you want to test highlighted in sys admin> preferences > general settings>Selectable themes.
You probably tried all this but that is as far as I can assist you. If that doesn't work then maybe one of the
smart Xoopsers will give you a helpful solution.
Good luck.