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One other thing to check is that the tyre is seated perfectly evenly on the rim.
Although to be brutally honest, I don't think you've got satisfactory clearance even if you can get the wheel to sit evenly, especially for use off road. There will be absolutely zero clearance for any mud/dirt and the occasional branch/twig. Why not drop down tyre size to a 35 or 38mm CX size? c.35mm is honestly plenty big enough for general offroad use.
Jameo-
Yes, you might well be right. I have actually got CX tyres that I've used before on the 700c wheels which worked well but I wanted to have a separate set of wheels to switch to rather than the faff of changing tyres. So I thought I'd try 650b and go a bit bigger with the tyre.
I've got some slightly smaller 650b tyres on the way and will take these tyres off and check how the rim is aligned.
motman
The wheel has Thru axles so definitely seated properly and my 700c wheels are perfectly aligned so sounds like the 650 wheel needs re-dishing.