I'm skeptical it's a chainline issue since 39-11 works well enough when running a double, and your 1X ring should be further outboard than a small ring in a double setup.

Have you double checked the high limit screw on the rear derailleur?

yeah I turned the limit screw all the way out just to make sure it wasn't that. It's hard to diagnose properly but I backpedalled slowly and that's when I noticed the chain catching on the 12t sprocket, I'm sure that could cause it to jump.

IMO, that's not a valid way to eliminate it as a potential cause. I have seen some derailleur hanger/freehub body/cassette combinations require the use of a small washer to move the RD out a hair.

3 ideas (in order of likelihood):

Bent derailleur hanger

chain too long

rear dropout alignment off.


Good luck
Andy

The 12 tooth cog can only 'catch' the chain when pedaling backwards, all setups do this to some extent.
The 12 tooth will only touch the chain near the point that the chain leaves the 11 tooth, so it simply cannot make it jump.
Is your hanger straight? The only correct answer to that question is 'yes, I aligned it with a hanger alignment tool.'
Is your B tension and chain length selected to allow the top pulley wheel to track the cassette properly?
Is your chain or cassette worn?
Did you align the derailleur on the 5th gear?
When you set the high limit screw did you align the centre of the top pulley with the outside edge of the 11 tooth cog?
Does it skip under high or low load?
Is there a tight link in your chain that only shows up under the tightest bend?

I'm going to throw this out there, cuz it happened to me one time: any chance you are using a 12t lockring with your 11-xx cassette? The 12t lockring has a larger diameter than an 11t lockring and caused the exact same problem when I wasn't thinking and put one on by accident...just a thought

Thanks all, these are some very helpful suggestions.

- I thought all lockrings were the same so I guess I might have a 12t on, I will check!
- I'll check the hanger alignment and chain length, could either of these cause it to jump in the 11t and work perfectly in every other gear?
- I don't think it can be the limit screw because I can 'micro shift' it past the midpoint of the sprocket
- It skips under low and high load, I can make it skip by lifting the rear up and turning the pedals by hand
- New chain but 2 month old cassette.......... however I rarely use the 11t sprocket so I don't think wear can be causing it.
- I will check B-screw and alignment of derailleur top pulley

Set the high stop exactly as I said, inline with the outside edge of the smallest sprocket. Set the low stop to be exactly in line with the centre of the first gear.
Then put it in 5th gear and tune it until it starts making noise trying to shift into the larger gear, then come back until it is quiet.
If you are within the capacities of the derailleur and everything is in line and no tight links etc, it will run fine.

Check your chain is around the right way and the joining pin is not sticking out or your joining link on the right way.
Make sure there are not too long hanger bolts interfering with the chain and that the inner derailleur cage is not on upside down.

lets not forget a possible loose hanger :)

both of my last 2 road bikes(with replaceable hangers) have ended up with shifting issues. both times, the flipping screws attaching the hanger has loosened significantly. guess they don't use Loctite at the factory

A loose hanger will not effect drivetrain.
The wheel skewer in most cases holds it all together and you only find out it is loose when you remove the skewer/wheel and it all starts to move........

both times I tightened that up and shifting returned to being crisp. I had thought the last time it was another cable devoured by shimano 10/11 spd STI. alas, I was wrong