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The rub was caused by a 25 GP4000 on a 17mm internal rim.
Changed to different 17mm internal with a 25 GP5000 and it was fine. Could have been a difference in lateral stiffness (?) of the rim. The first did seem to flex more when out of the saddle etc.
Also used 24 Turbo Cottons on a 17mm internal, which were fine.
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I think @dbr found 28mm 5k came up smaller than 25mm 4K but may have that wrong.
What rim/tyre combo caused the rub on the chainstay?