Record number extra trains (mostly special fare ones) have been introduced through out the year, introduction of flexifares, increase in Tatkal seats, Premium tatkal seats, increase incancellation charges etc, even then the revenue generation is down means some thing is wrong. possibilities could be
(1) Very poor occupancy of flexi fare, tatkal, prem.Tatka, suvudha, special fare seats
(2) possibility of some new kind of online fraud being through cancellation or something else done on IR as online transaction of tickets have drastically gone up.
(3)...
more...

Some thing else?

Unless over loaded IR can not get high number of passengers
Recent changes in cancellation and booking discouraged advance booking
Now people don't book to cancel latter as cancellation and booking charges are very high
Flexi Fare did more harm than good
2A/1A...
more...

fare are too high so unless it's urgency passenger avoids these classes
All Spl have high fare but Suvidha are mostly failed due to higher than Air fare.
The real and hidden income was Advance booking whom IR discouraged by making user unfriendly rules.