I have TS-112P and I did a firmware update to 4.1.0 a few days ago. From now on some applications' shortcuts at QTS desktop goes to one port
transmission => nas_ip:8081/transmission correct url http://nas_ip:9091/transmission
twonky media server => nas_ip:8081 correct url http://nas_ip:9000/
I can access the apps through correct URLs.
It happens only with specific applications: Transmission, Twonky, pyLoad, Tomcat, Optware. ...