That's what was happening on my bike. Runs fine on CR31's, but a random cylinder runs cold or not at all with the RS's.
I've tried running it on a full bottle with a large fuel line to verify it's not a fuel pressure issue, but the problem persists.
The one thing I haven't tried yet is to measure the amount of fuel that drains from the bowl on the cold cylinder and compare it to the amount of fuel on a running cylinder. Might be worth a look. IF the fuel level in low on that carb, it at least gives you a place to start looking.