Firstly, I take it you are using Advanced mode (i.e. at the top of the screen, you have clicked this).
To put it simply, RealTimeTrains displays what it's given, including anonymised freight paths, but these may just be from the Working Timetable (WTT) and indicate when there is an opportunity for them to run. If you click on the train's "FRGT" anonymised headcode, you can see a column marked "Realtime" updated when the train runs. If there is no column, there are no figures in bold or a red cancellation box appears, the train is probably not running - or will run later, under a different headcode/path or on a different route, but this is trickier to work out (e.g. the train may divert and not report where it's expected to, so won't be shown). You will also see some text at the top which may say "Runs as required" - this means that on a certain proportion of the days when the path is shown, it may not operate.
(Very) Short Term Plan or (V)STP paths are sometimes the best bet in terms of actually running, as these may be added for one-off workings or rarer paths, but they can also have their applicable trains cancelled.
Tom, who built and runs the site, does post on here and will tell you more, no doubt, if he sees this thread. All credit to him and others of the same mindset for working with the various powers that be to allow freight and NR train paths to appear, even if the trains don't exist in real life!
RealTimeTrains is under no obligation to display every train as running or not running at the instant you require the data, though it is a useful tool when used with discretion. I don't mean this to sound rude - just advice to make sure you don't treat it as the be all and end all of freight timetabling!
For the more knowledgeable and technically-minded members, I do appreciate this post is a generalisation and rather basic in terminology.