I don't know if it helps but I just added an updated Zone Rate Clone to:
https://www.zen-cart.com/downloads.php?do=file&id=977
that works with Zen Cart v1.5.0 - v1.5.4 at:
https://www.zen-cart.com/downloads.php?do=file&id=977
I don't know if this will correct your issues, but I have it working correctly on a Zen Cart v1.5.0 site ... you might try it and see if it resolves the problems that you are having ...
NOTE: the Zone Rate cloned files are different from the ones that you used so you might save your settings then uninstall your existing cloned shipping modules and delete them from the server in the directories:
/includes/modules/shipping
/includes/languages/english/modules/shipping
Also, after these are setup, if you could post the settings for each of the shipping modules that you see in the right hand panel, that would be a help ...
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