We've had nothing but issues since we upgraded from BorderManager 3.8 to BorderManager 3.9.

We get loss of connectivity frequently on remote applications (Citrix, PcAnywhere, etc).
YouTube videos start buffering at 1 or 2 minutes and never recover
All real time streaming videos with connectivity and drop problems
Downloads over 20 MB go from fast to slow to stalling completely
We cannot manage Proxy Configuration through iManager... we get a blank screen
This was an upgrade at first, but then a complete rebuild.

Our environment is...
Novell NetWare 6.5 SP8
BorderManager 3.9 SP2 with IR1
Latest TCPIP stack (domestic for VPN)
Latest NAT
Craig Johnson proxy.cfg
Tuning per BorderManager Proxy Performance Tuning Specs, except for maybe Proxy Configuration since we cannot access that screen
HP DL380 G5 Server with all the latest drivers

This all happens whether the filters are up or down. We are using static and dynamic NAT.