For a RailFan, watching MPS skips are far more interesting than watching F1 race - Prince Maan

It is usually ( I say 'usually', because in some cases it might be due to more political reasons, or the priority assigned to a zone for a train) not discrimination, but more about operational feasibility. I had learned a few things about his from a team at my college that worked on signalling system for Madras suburban network. They used to interact regularly with controllers during their work and had a good insight into how it works.
For trains that pass through multiple zones or divisions, usually the crew links, loco links, working time table, overtakes, crossings etc, are planned much in advance. So, when a train is running late, all the zones...
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the train passes through, will have to adjust their operations accordingly to accommodate the delayed train. For example, if 2 trains are headed towards CR and SCR from ET ( which is in WCR) via NGP, and both trains are running late/ or one of them running late, and if CR is able to accommodate a delayed train better than SCR, then priority will be given to the SCR bound train as any delay in that train would 'probably' result in a higher delay later on as SCR won't be able to accommodate it.
Usually we see some slack times at zone/division changeover points to accommodate such things, but the controllers are provided a delay margin for each train, using which they can associate priority to a train over the other.
Of course, some times, trains' controlling is also affected if it is a popular train on the route or through the zone ( i.e., one that the general public pay attention to) in which case, those particular trains are paid some more attention to ensure that a good image is retained in the public.
For the most part, controllers usually are just concerned with managing the trains in their sections, given the trains' TT requirements by all the zones/ divisions on their routes.