The ISP will only flip if you're transferring a ton of data.
I think this true for most of the IPS's. My ISP also doesn't allow keeping servers, but I've run Apache and FTP servers with my connection. It's just that they're not public. With exception of a few friends.
Basically, running any P2P program, hosting a net game or even using Skype means that you are technically running a server. What ISP's are really after, is denouncing resposibility of any user provided content by disallowing servers. They don't activilly search for users running servers and shut them down.