I have same issues with a device registered in V3 communicating over a gateway registered to V2. To my understanding, this should be supported.
In V2 I can send multiple messages, uplink and downlink work.
Moving the device to V3, I can send one message and downlinks don’t work. I do receive the first message though.
What I noticed is that in the V2 console’s traffic log of the gateway, I cannot see the downlink message which the V3 console claims it has sent. Taking a look at the downlink queue, the message was queued first, then gets removed. So I guess TTNv3 thinks it has sent the message.