This is all determined by your sort order for the order totals module, no?
If you have more than one type of tax, sort them in the correct order, so if there is a tax which the group discount does not apply to, that tax shows up before the group discount and is applied to the pre-group-discount total (group discount recalculate tax=none I think, as I've done mine below). This stuff is a bit hard for me to understand, actually, it gets my head spinning, so don't take my word for how this should work.
It occurred to me after posting my previous message that there are two meanings to "group discount" and I wasn't sure which you were talking about. ZC uses "group discount" to mean a discount that applies to a customer, who is a designated member of that group.
The other meaning is "quantity discount" which you set up in Attributes for a product. Say, if you buy at least 25 of item Z, you get 10% off the price.
I wasn't sure if you were talking about quantity discounts or group discounts.
---Diana