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and you have checked your task manager to make sure no instance was trying to load in the background? You mentioned doing a fresh install, though we just put out an update, please try manually downloading that one and see if that helps.
I suggest a fresh installation, and then do up your transfer settings from there. It might be because transfer settings got corrupted, or your settings are not correct, or you've too many pokemons in your inventory that fit the same category so it doesn't wanna transfer
if you mean its not transferring excess, by locking up then its because you have too many, try manually transferring some, and then rechecking your logic rules, typically that helps get things started again.
so i check and manually moved transferred and it still not transferring the ones it catches. I checked to see if there was something with the catching rule but there isnt one it just says transfer. and protect fav ones.