My experience may help. I have a BMC with Ultegra DI2. Everything worked perfectly until a flat caused a fall and bent the hanger. I replaced the hanger and indexed the gears according to Shimano (start at 5th cog, etc.). I fiddled with it a while, and eventually got it to shift smoothly, except that it would not go to the largest cog of the 11-gear cassette. All the other 10 gears worked fine, but it wouldn’t move up to that last one. I rechecked the hanger, adjusted the Low limit screw, but nothing worked. After a chat with my LBS, I realized what the problem was. While trying to index the derailleur in Adjust mode, I had somehow made the chain jump a gear (probably 15-20 clicks total in one direction) in Adjust mode. I didn’t think this could happen. Not realizing this, I had then gone on to index the gears correctly, but everything was now off by one whole cog. So for the Ultegra program, it would assume I had reached the last gear and so would not shift further, but in reality, there was still a gear/cog to go. I tested this by going through the gears in the opposite direction, and sure enough, at the last cog, it would try to still shift one more since it assumed there was still a cog left. I went back to Adjust mode, clicked until I moved the chain back over to the next cog, indexed again, and everything is perfect now.