If your Untangle protected network is suffering from random timeout issues. Check your Attack Blocker logs.
Anything in the list that has a reputation score greater than 80 points needs to be investigated. If it's a workstation, you've likely got a virus. If it's a server, take a hard look at the services running on the server. For SMTP, an exemption in the attack blocker may be in order to prevent the module from dropping packets. If it's HTTP, SMB, or any other protocol, a bypass rule is in order.
I just got off the phone with a client that was forwarding TCP 548, 3283, and 5900 to his xserve. The reputation of the xserve was over 400 points. Remove the server from the lan and the Internet smooths out...
It's time for an audit, and a reconfiguration. This module is your best friend for identifying badly configured network devices. Use it!