As per my personal experience,
01. Weather conditions effects more in North India.
02. Chain Pulling cases also more in north india.

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I have known from one of the persons of coolie union is that trains are sometime delibrately made to wait on the outskirts of NDLS station so that when crowd increases coolies can take advantage of crowd and make customers charge for their luggage more than the stipulated rate and also pick-pockteers are more active popular trains or famous trains have to arrive as they will get a good chance of stealing items and also giving their shares to railway officials and coolie unions.

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Well i am frm Karnataka.. once i was traveling with my uncle who is Guard.. The train was scheduled to depart at 3 pm but the station master was requesting for 10 mins more on walkie talkie to the guard.. my uncle denied.. SM said he asked the controller about it... wen my uncle asked him the Phone number of controller his mouth was shut..
just for collection of profit he was delaying the train..

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i travelled by Ganga Kaveri exp many times, every time from MAS to ET it runs well on time, from there on late to Allahabad by atleast 2-3 hrs ...
It cant b due 2 weather conditions or Chain Pulling cases as its Summer and travels ET-ALD section in nite

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GKP-LTT SF.. which doesnt stop at many stations.. 2yrs back i was returning frm LKO the chain was pulled 3 times on one day.. so jst imagine..

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