Craig,
How are your LAN clients configured? Are they configured to go through the Proxy server (Port 3128) or are you using the transparent proxy?
My guess is that your clients are connecting through the proxy. Each time you add/remove items from the custom list, the Squid proxy service gets restarted to force it to re-read the lists. So, since you're going through the Proxy server... and the server gets restarted, your connection is lost. A refresh brings the page right back up to the server-manager.
When connecting remotely, or from anywhere that doesn't specifically connect through the Proxy port... you won't notice the Squid service restarting, since you're just connecting through http.
Does that make sense?
Let me know if this isn't what's happening on your systems.
Thanks,
Abe