Hello Ekko,
In the first simulation there is no delay or channel effects, other than a small amount of simulated noise, so the data bits line up perfectly at the start of the error rate block. Now that you are transmitting over actual radios you have to account for all of the additional delay. That is your correct bit error rate right now, you are just not measuring what you expect. You will need to, at least, add packetising and some flow control to synchronize the inputs to the error rate block.