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The mech hanger doesn't appear bent
Yeah, but is it? Di2 just just suddenly shift different amounts so the only reasonable explanation is something has moved and the most likely culprit is usually the hanger (or loose cassette, or worn chain, but you addressed one of those issues).
I've never updated firmware on any of my Di2 and they all just work. If it was the extremity cogs I'd suggest your limit screws were off but because it's kinda in the middle of the cassette it does sound more like something is piss.
hippy-
+1
If your di2 shifting gets a bit wonky, it's almost always a bent hanger. Once you have the indexing and limit screws set up properly they will always be good because there are no cables to stretch, the derailleur always shifts the same distance and the rear spacing/spacing between cogs doesn't change.If a hanger alignment doesn't fix it the only other thing that causes issues is a gunked up/worn tension spring which will affect how your derailleur moves as you shift up and down the cassette. Easy to pull it apart to check and replace if needed.
amac090
Recently my bike with di2 has been slow to shift down the cassette (to the smaller cogs), but only for 3 specific cogs: 2nd largest to 3rd, 3rd to 4th, and 4th to 5th. Shifting up the cassette is very quick. Shifting down across all other cogs is fine.
The chain was just over 50% worn so I replaced it. However, the issue persists, and I've now realised it does it across 3 different cassettes (2 wheelsets and turbo).
The mech hanger doesn't appear bent, and is only about 18 months old. The derailleur appears to be tight on the hanger. I've had the bike for 3.5 years now and shifting has always been perfect until a week ago.
Any ideas to help me diagnose and fix the issue? I'll plug in eTube and update the firmware if it needs it later. However, I'm struggling to think why/how there could be an issue with just 3 downshifts. Typically a bent hanger, or needing to micro-adjust, would result in the shifting being off over the whole cassette.