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I just removed the rear wheel to get a new tire fitted. The lower pinch bolt on the left side eccentric was really hard to undo. I got it out after heating things up a bit but the threads on the bolt look damaged. I used one of the other bolts to check that the threads in the swingarm were OK and I noticed that the bolt would only screw in about 2/3rds to 3/4 of its length before it hit a dead stop. Checked the right side lower and found the same. So I'm guessing the two lower holes in the swingarm are only threaded part way, so have to be careful not to over-tighten the two lower bolts (which I think is what damaged the threads on the left side bolt). Has anyone else come across this?

Yeah ,because they are poxy to get at some peeps will X tread the bolts and bugger the threads , then they try and helicoil them and get the insert in off square .......
Can of worms I know but I would remove the swing arm (doesnt hurt to service the pivot ) and get it in a vice nice and level where you can inspect properly and hold a square up to it and fix all the threads ( its unlikely that only one got damaged ) . You dont get many goes at this before the swing arm is toast.
A bit of mucking about but if you fix this properly now and remain aware of the issue this will never give you problems again .
While your at it make sure your rear sprocket is secure .....bolts have come loose and chewed swing arms . There are posts re this .