A double press of Stop clears the Bookmark from the video. Nothing else.
If you are switching Zones to play media, such as to a Video Zone to play a movie, MC always leaves the last playlist in that Zone, when you switch out to another Zone. At least for me. In fact, sometimes I clear Playing Now, and the reference to the file disappears, but the thumbnail image stays in Playing Now until I refresh the View.
There is a setting in "Options > General > Advanced > Clear playing now on exit", but if you never exit MC, and just leave it running like most of us do, that won't clear Playing Now for the Zone. It only clears on exiting the MC application.
You could try "Options > General > Behaviour > Remove file from Playing Now after they are played", but that may require playing to the end.
Then there are two other settings that may impact this;
"Options > General > Behaviour > Double-click" when set to "Replace Playing Now (All)" will clear the previous movie from the Zone, if you start the new movie using a double click, which perhaps JRemote emulates?
"Options > General > Behaviour > Play Button" setting choice may change what you see. i.e. If set to "Play visible files" you may never see Playing Now, and combined with the above settings, never know the old movie had still been in the Zone. If set to "Play Playing Now" you may have seen the Zone and the previous movie.
Have you changed any of the above settings?
Are you sure the behaviour has changed? Or have you just noticed the movie hangs around for the first time?
Does it really matter? That is, does the previous movie play when you don't intend it to?