I tried with your fix (input.rewind() instead of input.setInputStream(...)) and I have an immediate exception launching the TestServer from the project I attached in my first post.
setInputStream is setting the limit=0, and rewind is not .. so that's maybe the reason :)
00:00 TRACE: [kryonet] Server listener added: test.TestServer
00:00 TRACE: [kryonet] Server thread started.
00:00 INFO: [kryonet] Server opened.
00:00 TRACE: [kryonet] Connection listener added: test.TestServer$ClientListener
00:00 TRACE: [kryonet] Client listener added.
00:00 TRACE: [kryonet] Client thread started.
00:00 TRACE: [kryonet] Connection listener added: com.esotericsoftware.kryonet.Server$1
00:00 TRACE: [kryonet] Connection 1 sent TCP: RegisterTCP (6)
00:00 DEBUG: [kryonet] Port 59520/TCP connected to: /
127.0.0.1:66600:00 TRACE: [kryonet] Connection 1 received TCP: RegisterTCP
00:00 TRACE: [kryonet] Connection 1 sent TCP: RegisterUDP (6)
00:00 INFO: [kryonet] Connection 1 connected: /
127.0.0.100:00 ERROR: [kryonet] Error updating connection.
com.esotericsoftware.kryonet.KryoNetException: Incorrect number of bytes (2 remaining) used to deserialize object: com.esotericsoftware.kryonet.FrameworkMessage$RegisterTCP@1922221
at com.esotericsoftware.kryonet.TcpConnection.readObject(TcpConnection.java:150)
at com.esotericsoftware.kryonet.Client.update(Client.java:246)
at com.esotericsoftware.kryonet.Client.run(Client.java:324)
at java.lang.Thread.run(Thread.java:662)
00:00 TRACE: [kryonet] Unable to read TCP from: Connection 1
java.net.SocketException: Connection is closed.
at com.esotericsoftware.kryonet.TcpConnection.readObject(TcpConnection.java:109)
at com.esotericsoftware.kryonet.Server.update(Server.java:197)
at com.esotericsoftware.kryonet.Server.run(Server.java:355)
at java.lang.Thread.run(Thread.java:662)
Exception in thread "Client" com.esotericsoftware.kryonet.KryoNetException: Incorrect number of bytes (2 remaining) used to deserialize object: com.esotericsoftware.kryonet.FrameworkMessage$RegisterTCP@1922221
at com.esotericsoftware.kryonet.TcpConnection.readObject(TcpConnection.java:150)
at com.esotericsoftware.kryonet.Client.update(Client.java:246)
at com.esotericsoftware.kryonet.Client.run(Client.java:324)
at java.lang.Thread.run(Thread.java:662)
00:00 INFO: [kryonet] Connection 1 disconnected.
java.net.SocketException: Connection is closed.
at com.esotericsoftware.kryonet.UdpConnection.send(UdpConnection.java:99)
at com.esotericsoftware.kryonet.Client.connect(Client.java:179)
at com.esotericsoftware.kryonet.Client.connect(Client.java:110)
at test.TestServer.start(TestServer.java:29)
at test.TestServer.main(TestServer.java:64)
Patrice.