Further update: possible problem found.
taxes_controller.class.php
The line 100:
/* Only subtract if coupons apply to tax. Likely in 4.0 */
/* $total_tax -= $coupon_tax; */
The problem here is that although the option to apply coupon to tax is to be introduced likely in version 4.0, already the calculation has changed.
Please revert this calculation until the option is added!