&gt; To make this even more mysterious, this problem only occurred in one of our data centers, and we narrowed it down to the router being the only difference. Replacing the router also &quot;fixed&quot; the issue.<p>Did you confirm the packets were the same on both sides of the router? This pattern sounds like possibly network microbursts, which can lead to dropped packets -- maybe the replacement router had a larger buffer so you didn&#x27;t drop any packets, and things worked better.<p>I&#x27;ve also seen some exciting bugs with SYN cookies on other platforms, it&#x27;s possible there&#x27;s some encoding error leading you to a very small window -- something wrong with the window scaling negotiation perhaps? If you&#x27;ve got enough incoming syns that syn+ack state is being dropped (so syncookies are being used to finish the connection), you&#x27;re also going to not retransmit syn+acks, so then you need to wait for the SYN to be retransmitted.