Thanks for all the help and comments. I have started using the 
ip_conntrack_amanda module in my iptables setup and that seems to work 
fine.

The issue of stock packages vs. personalized compiles is an interesting 
philosophical debate I'd rather not get into at this point. Both 
approaches have their merits, and both are appropriate under certain 
circumstances. I prefer to use stock packages where they provide enough 
power and flexibility to solve the problem at hand. The combination of 
amanda, iptables, and ip_conntrack_amanda does that for me in this case. I 
understand that YMMV.

Thanks again to all.