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Looks like the old AS400 was tweaked to use an MTU of 1492 instead of the standard 1500. The new AS400 is using an MTU of 1500.
As the FTP server now assumes it can send 1460 bytes segments, it does so and two of these are missing (there is a gap of 2920 bytes in the TCP stream). As they are not received, they are not ACKed, so they are retransmitted from the server side, but again too big, so these segments never arrive at the (new) AS400.
Have a look at the NIC and TCP settings of the old AS400 and the new AS400 and make sure they match. I expect that only the MTU needs to be lowered to 1492 (1492 is seen on connections that use PPPoE, as the PPPoE header is 8 bytes and will be added to all packets).