I'm running 1.3.9d and still have the same tax problems as in 1.3.8 involving tax calculation and group discounts
The issue is said to be solved in 1.3.9 but it isn't

Here's what's happening:

These results are all correct when buying a product with free shipping:

Sub-Total:€16.95
Free Shipping Options (Free Shipping):€0.00
Group Discount:-€5.09
TAX 6%:€0.67
Total:€11.86

I was very happy about this, since this wasn't working correct in 1.3.8. But now there's the problem when adding shipping costs/tax

Once I choose flat rate shipping (TAX 19%) it messes up everything:

Sub-Total:€16.95
Flat Rate (Best Way):€5.65
Group Discount:-€4.82 -- incorrect
TAX 6%:€0.81 --incorrect
TAX 19%:€0.76 --incorrect
Total:€17.78 --incorrect

I've tried every sort order in ordertotal, every config in shipping and in grouppricing, nothing seems to help.

Please reopen this issue, or please help me with this.

Greetings Antonios