bad ACK response to SYN

I'm having a problem with a web server, which causes the web client to occasionally throw a Connection refused exception despite the server being up and listening. This seems to happen when the rate of socket establishment from the client is high enough that the client is reusing ephemeral ports roughly every couple minutes.

In packet captures, I note the following unusual sequence around the time of the Connection refused exception:

Client -- SYN -> Server

Client <- ACK -- Server

Client -- RST -> Server

The server replies to SYN with ACK, rather than SYN,ACK. Furthermore, in this ACK, the acknowledgement number is not the SYN sequence number plus one. Rather, it is the same acknowledgement number last sent by the server in the previous socket that used the same client port. This acknowledgement number falls outside the window, thus eliciting a RST response from the client.

Wireshark seq/ack analysis marks the erroneous ACK with [TCP ACKed unseen segment] and shows the RST cause as TCPS_SYN_SENT-Bad_seq

For this service, the server initiates socket close, so all the sockets have the following closing packet sequence:

1) Server -- FIN,ACK -> Client

2) Server <--- ACK ---- Client

3) Server <- FIN,ACK -- Client

4) Server ---- ACK ---> Client

and in the problem cases, the acknowledgement number from (4) above is repeated much later in the server's ACK response to the client's SYN request for a new socket.

The server is running RHEL, and the TIME_WAIT interval is 60 seconds. When I see the problem behavior, the client SYN is sent more than 100 seconds after the closing sequence from the previous time the ephemeral port in the SYN was used, so from the server's point of view the previous connection should be fully closed.

It looks as if the server sometimes loses track that a connection is closed. Any ideas on what might be wrong?

Thanks!