I have the following scenario:
Two Windows Server 2008 are communicating in a client/server fassion with a Juniper ISG 1000 (6.3.0r6) in between. The client is creating around 100 new tcp connections per second. After some time (minutes) the firewall seems to block new connections (SYN packets are sent but does not arrive at the server). Only some new connections are blocked, like 1-3 / sec. As far as we can see the firewall has no IDP turned on and it's not logging anything interesting.
If we close the client/server app and then run netcps (sends random tcp data) on that same port it get connection timed out. On another port it works. That should exclude errors on Ethernet or IP layer.
Update: We are reproduce this using nping to send around 60 tcp handshakes / second. It takes a couple of minutes to reach a state where most or all connections are timing out. Sniffing in the Juniper firewall using both flow debugging and snoop does not show any of the failed connections :(. Same behavior between servers without a firewall in between works fine.