I haven't used the Nike shirts you mentioned, have done some Under Armor, but have never noticed a fading. Usually, certain colors darken temporarily with heat, not fade.
Do they do the same thing in a conveyor dryer? Also, do you have some specific products that faded while others didn't?
I looked into this a bit with Nike, and got very little direct help, but do see that their recommendations for screen printing are on their website:
Can I screen print on Dri-FIT fabric?
Yes, you can screen print on Dri-FIT fabrics. However, in order not to diminish the performance you must:
Use water based inks whenever possible
Print only small areas and fine lines with lots of open space so that there are no large areas of coverage. The ink blocks the moisture absorption and breathability of the fabric, reducing the effectiveness of Dri-FIT garment(s).
That. and their instructions for ironing with a cool iron are the closest I could come to any decoration tips.