Ashish, you are not the only one. The same happened with me also way back in 2010. I had flight on Saturday from Bangalore to Guwahati via Kolkata and then train ticket on the same day from Guwahati to my home town.
Due to fog, Bangalore flight got delayed and I missed the Guwahati flight from Kolkata and so the train from Guwahati. I stayed back at Kolkata and then took the next morning flight for Guwahati.
But much to my surprise, i was refused refund for the Saturday's train ticket, even after providing the copies of my boarding passes as the evidence that I did not travel on Saturday.
The IRCTC's logic is that I did travelled by train on Saturday from Guwahati to my home town (7 hrs journey) and then from my home town I managed to reach back Kolkata again (10 hrs journey) for no reason and again took Sunday's flight for Guwahati. Even, when I shared the phone numbers of the concerned airport authorities and the hotel, where i stayed full Saturday at Kolkata, they stopped replying to my mails. Such an unprofessional behaviour.
I am sure these type of things happened with many others and its high time that we atleast post the same on online forums and even approach consumer court.