I was going to suggest you do a systematic step-by step check of one engine/clutch assembly against the other -it's very easy to miss something unless you are absolutely meticulous.
"Dry assemble" the clutch onto the shaft without the chain to ensure that nothing is binding - such as an incorrect washer that could be stopping the clutch drum from spinning freely by binding against the crankcase. Even a grossly misaligned chain shouldn't be causing this (it wouldn't help matters tho'), but if the chain is too tight and you've got tight spots in it due to a bent axle, that might be enough to overload the clutch bearing. You say they are seizing -do you mean the clutch bearing is failing and locking the drum to the clutch hub?
By the way, are you mounting the clutches in the conventional way with shoes and open side of the drum facing out, or reverse mounting it?
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