Ah, yes...the quest for perfect shifting...We had the same problem with 11 speed eTap. Our 11-40 and 52-34 + roadlink just never quite shifted right. Almost the exact symptoms you are describing...will shift one way but not the other. I have to say that when the chain was brand new, and matched to the cassette (shimano-shimano or Sram-Sram) it all worked better for a while. A little wear or grit and things were off again.
Eventually I changed the entire system to XTR 3x11 with a 30-39-52 and 11-42. This was much better...when the FD was adjusted just right, but this had a tendency to get out of alignment, so shifting up to the 52 or down to the 30 sometimes became problematic. This also became frustrating, so I changed the FD to a 2x XT unit, dropped the rings to 48-34, and changed the rear freehub from shimano to XD and I am using a 10-42. Now this does work well. the FD only has to deal with 2 rings, so more room for imperfection. the rear with a little b-screw adjustment sits just right on the cogs. This gives almost the same low and a little over the previous high gear. Next experiment is to attempt to drop the inner chainring to 30t which delivers about 18" low gear for those 15% grades around our area in the Pacific NW.