Charlie,
I used the port forwarding rules in the SnapGear to move all port 443 traffic to the SME server, and that worked wonderfully for quite some time.
Once I noticed the SynFlood traffic coming from my satellite offices, I moved them from WebMail to Outlook Express using IMAP over SSL. Strangely, I still see SynFlood traffic coming from those IPs.
Unfortunately, documentation on the SnapGear has always been thin, but I did just find this after a little hunting:
If SynFlood or Flood appears repeatedly in the system log, it means the SnapGear is receiving more than 5 incoming connections per second, and believes it is being attacked. For security, it then ignores any additional incoming connections.
There was also a fix listed for it, so I'll try that and see if it solves the problem. It might just be that WebMail by nature entails a lot of separate HTTPS requests which are mistaken for threats.