I just tested it again on a fresh install and it is defiantly this plugin, the fresh install only included WooCommece (latest version), this plugin (again latest version) and a query monitor to debug.
The coupon was set to Individual use only.
The Cart Cross-Rule Limits rule was set to “No cart Rule Discount Limit”.
The coupon used would show in the basket totals, with the price rule not in the totals, however the price rule table breaking down this discount still showed along with a Woocommece warning saying that the coupon has already been applied (it hadn’t) and can’t be used with other coupons (it was the only coupon being applied in the totals).