I run a DC++ server (PtokaX) with peak users around 1500. From time to time, the server goes in a state where any new socket connection to PtokaX stays at SYN_RECV and few sockets at CLOSE_WAIT. I am sure the problem is application specific since ssh responds normally. Also my network connection at that time is perfectly stable as well (checked with ping).
I am sure it is not a SYN flood since the sockets in SYN_RECV state are from all different ips. Also my own connection stays in that state. I am using Debian 6.0.3 linux 2.6.32-5 i686.