Ok, I see. You're not tunneling "internet traffic", but HTTP (web) traffic. And only SOCKS capable programs that are configured to use SOCKS will be using the proxy.
You may not be aware of this, but your ISP will still see the places you might be visiting (if they wanted to), as your DNS requests go out over their lines unencrypted. So they'll see your requests for addresses such as stealingmovies.com or skinnydippingdogs.com.
At any rate, none of this is relevant to MC's library server, as it is not communicating using the HTTP protocol.
It is likely that the problem you are experiencing is due to using the access key, where MC does use HTTP to connect to JRiver's server in order to broker the connection between your work and your home's MC system. You don't need to use the access key method, and can instead use your home's WAN IP address. Keep your router's port forwarding 52199 as you've had it and use Library Manager to connect to a library at your WAN IP address.