Perhaps the cable has stretched? Or the cable settled properly into the external part of the hub.
This is what I do for my Alfine 8 speed.
1. Remove cable from hub.
2. Set barrel adjuster on the lever to the middle of its range
3. Measure how far the nut on the cable that engages with the hub is and ensure that it is the correct distance. From memory it’s 102mm on the 8 speed, but I cold be wrong and it’s probably different for the 11 speed but the same principle should apply.
4. Adjust nut position if necessary.
5. Re-engage nut and select the correct gear for aligning the dots (it’s 4th on the 8 speed, don’t know what it is on the 11). The dots should be pretty close if you’ve selected the right gear.
6. Fine tune as required using the barrel adjuster