the hardest part of a bird flying is the take off and needs enough uplift to get of the ground , yes i believe muscles wont be strong after the lock up and in order to build muscle the muscles have to damage creating microscopic tears in the muscle which needs protein and calcium to repair , so only thing i can think of is the birds diet needs to be correct to make sure there not too fat before forcing exercise upon them and give plenty of calcium and protein to get them to fitness , the only thing i could think of is these birds have been treated with antibiotics , the antibiotics stop the immune system from working whilst the drug deals with the problem .After a course of antibiotics you should follow up with a probotic my probotic of choice is Live Natural yoghurt , Brewers yeast has every possible vitamin your birds need , and a product im never without