They are likely not in pain initially but it is uncomfortable to stand long on two legs. The hips are shaped differently so the back legs naturally point forwards instead of down when standing on two legs. So they can not stand straight up. They are basically doing a squat. And just like when you are doing a squat it is a bit uncomfortable and you would not want to do it for long. But it is not actually painful until you do it for too long.
Of course it is different for different animals. Bears seams to be more comfortable on two legs then most animals. A lot of animals can not even get their legs bent far enough to balance over them and are therefore unable to stand on two legs at all.
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